Table 1

Box C/D snoRNAs identified in N. crassa

Homologs

Namea

Lenb

Chrc

Expd

Target site(s)

Matche

G pf

S. p

S. c

A. t

H. s

Locationg


Nc CD1

125

III

C, N

26S-Am2242

10/0

D'

-

snR13

-

-

Intron

Nc CD2

99

V

C

26S-Um2379

13/0

D'

snR66

snR66

-

-

IR

Nc CD3

90

I

C, N

26S-Um2840

14/0

D'

-

-

snoR29

Nc CD4

81

V

C, N

18S-Cm49

13/0

D'

-

-

-

-

Intron

Nc CD5

80

VI

C

26S-Am856

10/0

D

snR60-I

snR72

snoR72Y

-

Intron

26S-Um2383

12/0

D'

snR78

snR78

snoR37

U52

Nc CD6

76

I

C

26S-Um2687

11/0

D'

snR51-I

snR51

-

U41

Exon

Nc CD7

84

VI

C

26S-Gm2250

12/0

D'

snR75

snR75

U15

U15

Intron

Nc CD8

85

I

C

26S-Gm2751

13/0

D'

snR48

snR48

-

U60

IR

Nc CD9

81

I

C

18S-Gm1122

14/0

D

snR41-II

snR41

-

-

Intron

Nc CD10

104

I

C, N

26S-Um1039

12/0

D

-

-

-

-

Intron

26S-Am3264

13/0

D'

-

-

-

-

Nc CD11

79

I

C

18S-Am793

13/0

D'

snR53

snR53

snoR53Y

-

Intron

U6-Am47

11/0

D'

snR53

-

-

mgU6-47

26S-Am356

15/0

D

-

-

-

-

Nc CD12

85

VI

C

26S-Cm2159

10/0

D'

-

snR76

Ath119b

HBII-180

Intron

Nc CD13

84

VI

C

18S-Am538

12/0

D

snR41-I

snR41

snR41Y

U62A/B

Intron

Nc CD14

75

IV

C

26S-Am2288

10/0

D'

-

-

U79

U79

Intron

Nc CD15

73

I

C, N

18S-Am159

11/0

D'

-

-

-

-

Intron

tRNAThr-Um114

12/1

D

-

-

-

-

Nc CD16

122

II

C

26S-Gm2357

13/0

D'

snR81

snR190

-

HBII-99

Intron

26S-Gm1907

D'

-

-

-

U50

Nc CD17

73

I

C

18S-Am154

13/0

D

-

-

-

U45A/C

Intron

26S-Gm2875

12/0

D'

-

-

snoR34

HBII-210

Nc CD18

88

V

C, N

18S-Cm1004

11/0

D

snR79

snR79

-

-

Intron

Nc CD19

75

III

C

18S-Gm1423

13/0

D'

snR56

snR56

snoR19

U25

Intron

Nc CD20

75

VI

C, N

26S-Um2372

13/0

D

snR88

-

snoR58

-

Intron

Nc CD21

69

VI

C

18S-Am28

13/0

D'

snR74

snR74

U27

U27

Intron

Nc CD22

79

I

C

26S-Um1866

14/0

D'

snR62

snR62

U34

U34

Intron

18S-Um893

11/0

D

-

-

-

-

Nc CD23

72

V

C, N

26S-Gm2773

11/0

D'

snR38

snR38

snoR38Y

snR38

Intron

Nc CD24

75

VI

C

18S-Um575

13/0

D'

snR77

snR77

snoR77Y

HBII-135

Intron

U5-Am62

15/0

D

-

-

-

-

Nc CD25

81

I

C, N

26S-Am846

13/0

D'

-

-

-

-

Intron

Nc CD26

77

I

C

U2-Gm183

11/0

D'

-

-

-

-

Intron

Nc CD27

85

VI

C

26S-Am2904

15/0

D'

snR71

snR71

U29

U29

Intron

26S-Cm2906

15/0

D'

snR69

snR69

snoR69Y

-

Nc CD28

78

II

C

26S-Am1845

12/0

D'

-

-

snoR33

U95

Intron

26S-Am1859

14/0

D

-

-

-

-

Nc CD29

101

II

C

U2-Am31

16/0

D

-

-

-

SCARNA9

Intron

5.8S-Am42

14/0

D'

-

-

snoR9

-

Nc CD30

84

I

C, N

18S-Cm584

12/0

D'

-

-

-

-

IR

Nc CD31

101

VI

C, N

26S-Cm2917

13/0

D'

snR73

snR73

U35

U35

Intron

Nc CD32

82

VII

C

18S-Am161

11/0

D

-

-

snoR18

U44

Intron

18S-Um167

11/0

D'

-

-

snoR122

U45A/B

Nc CD33

102

III

C

26S-Am2218

13/0

D

snR63

snR63

U46

U46

Intron

Nc CD34

69

IV

C

18S-Um1265

12/0

D'

snR55

snR55

snoR34

U33

Intron

Nc CD36

90

I

C

26S-Cm2299

10/0

D'

snR64

snR64

snoR44

U74

Intron

Nc CD37

97

II

C

Cleavage

U14

U14

U14

U14

Intron

18S-Cm411

15/0

D

U14

U14

U14

U14

Nc CD38*

80

IV

C

26S-Am1114

12/0

D'

snR61

snR61

U38

U38

Intron

26S-Am2858

10/0

D'

-

-

-

-

Nc CD39

73

I

C

26S-Am897

13/0

D'

snR83

-

-

-

Intron

26S-Am375

11/0

D

-

-

-

-

Nc CD40

107

IV

C, N

26S-Am2062

11/0

D'

-

-

-

-

Intron

Nc CD41

72

II

C

18S-Gm1423

12/0

D'

snR56

snR56

snoR19

U25

Intron

26S-Cm1489

12/0

D

-

-

U49

mgh28S-2409

Nc CD42*

92

II

N, R

18S-Am417

12/0

D

snR52

snR52

-

U83

Intron

Nc CD43

96

VI

N, R

18S-Gm559

11/0

D'

snR80

-

-

-

Intron

Nc CD44

85

IV

N, R

18S-Um1227

15/0

D'

snR82

-

snoR14

HBII-55

Intron

26S-Cm776

11/0

D

-

-

-

-

Nc CD45

102

I

N, R

26S-Um3021

11/0

D

-

-

-

-

IR

Nc CD46A

89

VII

N, R

26S-Am635

11/0

D'

U18

U18

U18

U18

Intron

Nc CD46B

89

I

N, R

26S-Am635

12/0

D'

U18

U18

U18

U18

Intron

Nc CD47*

75

III

N, R

26S-Gm785

16/0

D

snR39b

snR39b

snR39BY

snR39b

Intron

Nc CD48*

91

V

N, R

26S-Am797

14/0

D'

snR60-I

snR60

U80

U80/U77

Intron

26S-Gm888

17/0

D

snR60-II

snR60

U80

U80

Nc CD49

91

I

N, R

26S-Um2682

12/0

D

-

snR67

-

-

Intron

18S-Am971

13/0

D'

snR54

snR54

U59

U59A/B

Nc CD50

98

I

N, R

26S-Cm1418

15/0

D'

U24

U24

U24

U24

IR

Nc CD51

87

VII

N, R

26S-Am1430

13/0

D'

U24b

U24

U24

U76

Intron

Nc CD52

177

VII

C, N

tRNA-Am43

11/0

D'

-

-

-

-

IR

tRNALeu-Am90

12/0

D'

-

-

-

-

Nc CD53

212

IV

C, N

Orphan

-

-

-

-

IR

Nc CD54

125

V

C, N

26S-Um667

10/0

D

-

-

-

-

IR

Nc CD55

137

IV

C, N

Orphan

-

-

-

-

Intron

Nc U3A

262

I

C, N

Cleavage

-

-

-

-

RE

Nc U3A-2

184

I

C, N

-

-

-

-

RE

Nc U3A-3

75

I

C, N

-

-

-

-

RE

Nc U3B

270

I

C, N

Cleavage

-

-

-

-

RE

Nc U3B-2

191

I

C, N

-

-

-

-

RE

Nc U3C

275

II

-

Cleavage

-

-

-

-

RE


a The box C/D snoRNAs were numbered according to the order of identification. b Len, cDNA length of the snoRNA. c Chr, chromosomal location of snoRNA gene. d Exp, expression situation. C, N, R, snoRNA was identified by cDNA library, northern blotting analysis, and reverse transcription analysis, respectively. e target match, (Watson-crick pairs+G*U)/mismatch. f Gp, guide position. g IR, Intergenic region; RE, Repeat element. The genes marked with asterisks indicate that the genes were annotated in the Neurospora crassa database but were not detected by experimental methods. The data for S. p snoRNAs were cited from Luo (2004) [38] and Bi et al. (2007) [39]. A. t snoRNAs and modifications are from the plant database http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/conservation webcite. S. c snoRNAs and modifications are from the yeast snoRNA database at UMass-Amberst http://people.biochem.umass.edu/fournierlab/snornadb/main.php webcite. Abbreviation: S. p, S. pombe; S. c, S. cerevisia; A. t, A. thaliana; H. s, H. sapiens.

Liu et al. BMC Genomics 2009 10:515   doi:10.1186/1471-2164-10-515

Open Data