ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatatttaaatttattctgcttgctgtttttttttgtgatattgctttgggtgaacaattgagcatttgtgatgattttctgttatcag

Basic information

species	Zea mays
transcript	GRMZM2G090738_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 5

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatatt-taaatttattctgcttgctgtttttttttgtgatattgctttgggtgaa-caattgagcatttgtgatgattttctgttatcag
| |||||||||||  | ||| ||||||||||||| |||| | |||||| |||||| |||||||| |||||||||||||||||| || || ||    |||  |   |||| |||   ||||  |  |  |  |||| ||| | ||  |||  |  |||  ||                        
CTTACTGCACTGGCTTGCTTCTGGCTCGTCGTGTGCTCACGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATGTTGAGgtacaaatataatccttataatttttttactctatatgctcatgctggtcttgatcttgatatgtatgattcctttggtcag-----------------------

upper sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 5'ss of exon 5

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatatttaaattt-attctgcttgctgtttttttttgtgatattgctttgggtgaacaattgagcatttgtgatgattttctgttatcag
| || ||||||||  | ||||||||||| ||||| |||||| |||||| |||||| |||||||| ||||||||| |||||||| || || ||    |||  |  ||| | |||   ||||  |  |  |  |||| ||| | | | |    |  |||    ||  | |                
CTTATTGCACTGGCTTGCTTTTGGCTCGCCGTGTGCTCAAGCTCCGTGGTTTGGACCAGGAGTACGAGGGCAATATTGAGgtacaaatacaatccttataaattttttactctatatgctcatgctcatgctgattttgatcttgatatgta--tgattcctttggttag--------------

upper sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 5'ss of exon 5

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatatttaaatttattctgcttgctgtttttttttgtgatattg--ctttgggtgaacaattgag-catttgtgatgattttctgttatcag
| ||||| ||||| ||||||||||||||||||||||| || || |  ||  ||||| | ||||| ||||| || || ||||||   |   |     | ||| | || ||  ||             ||     | ||   |||| | | || || |||  ||    |||||| |            
CTTACTGTACTGGCCTTCTTTTGGCTCGTCGTGTTCTGAAAATGCTGGAAATGGATGATGAGTACGAGGGAAACGTAGAGgtatgttgtga-----tcttttatttcatcttgaaaataaagaaacttgagagttttcatcttttgattaataactgaatcaaaattgatgaatcag---------

upper sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S38_329V6.1 (Physcomitrella patens), 5'ss of exon 6

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatat--ttaaatttattctgcttgctgtttttttttgtgatattgctttgggtgaacaattgagcatttgtgatgattttctgttatcag
| || ||||||||||||||||||||||||||   | | |||| |   || ||||||||||||||||  || || |    |||     |  |     | |  || |  |  |||||     ||| |       |  ||||  ||||  |    |  |  |  | |||     || | |  | |   
CATATTGCACTGGTCTTCTTTTGGCTCGTCGGCATTTGAAGAACTTCGAGTTGGATCAGGAGTATGTTGGGAACGAGACGgttcgtgtgtagtctttctgcttgacctcgttctgaccattgtatcagcaattactatt--tttgattttgtatctacgtttgtgtacaatttgtatactgt---

upper sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S371_31V6.3 (Physcomitrella patens), 5'ss of exon 4

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaaaacaaatatttaaatttattctgcttgctgtttttttttgtgatattgctttgggtgaacaattgagcatttgtgatg-attttctgttatcag-
| ||||||||||||||||||||||||||||||  | | ||||     || ||||| |||||||| |  |||||||    |||    ||    |  || |||   |||      |||  ||    || | ||||   | ||| |  |       |   || ||| | || |      |||    | 
CTTACTGCACTGGTCTTCTTTTGGCTCGTCGTCATTTAAAGAATTTCGAGTTGGACCAGGAGTACGTAGGCAATGAGACGgt----ttgtttcttatcttttcctttccataccttcatgaagattgtagtgaccct-cttggttttgtggggttcacacttgcgttggacacaaggttgattgt

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|211279083|gb|FL069189.1|FL069189

EST:     GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG                         GCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

EST: gi|60395892|gb|DN228762.1|DN228762

EST:     CAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG                         GCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: CAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

EST: gi|60345048|gb|DN212021.1|DN212021

EST:     AGGGCAATGTTGAG                         GCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: AGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

EST: gi|32846847|gb|CD986528.1|CD986528

EST:     GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG                         GCCATTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

EST: gi|211279085|gb|FL069191.1|FL069191

EST:     GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG                         GCCACTGGTGA
genomic: GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGA

EST: gi|67024091|gb|CO452840.1|CO452840

EST:     GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG                         GCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

EST: gi|60672209|gb|DN474977.1|DN474977

EST:     GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAG                         GCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: GTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

EST: gi|60347188|gb|DN214161.1|DN214161

EST:     ATCAGGAGTATGAGGGCAATGTTGAG                         GCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC
genomic: ATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTC

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 156

CCTACTGCACTGGTCTTCTTTTGGCTCGTCGTGTTCTCAAGATCCGTGATTTGGATCAGGAGTATGAGGGCAATGTTGAGgtaaaattaa ... ctgttatcagGCCACTGGTGAGGACTTCTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTG

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72