ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgcccacgatctgtctctgaatgcttttgatttttttttgcccgtagtttcgtctcagctgatgtgcgttgttgctgcgcgtcaacgattgtgaca...

Basic information

species	Zea mays
transcript	GRMZM2G041797_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G041797_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 5'ss of exon 1

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgcc----cacgatctgtctc-tgaatgcttttgatttttttttgcccgtagtttcgtctcagctgatgtgcgttgttgctgcgcgtcaacgattgtgaca
||| || |||||||||||||||||||| ||||| ||||| ||||||||||| ||||| || |||  ||| ||||||||||||||  |||||||| | ||||| | |||       || |  ||||   |||  |     || || ||  | | |   |||   |||   | || |  ||     |   ||       ||  |   
CATCCCTTCCTTCAAGATCTACCGCGGCGTCGCCGGGCTGTACGACTACGGCCCGCCGGGATGCGCCGTCAAGGCCAACGTGCTCGCCTTCTGGAGGCAGgtcaggccgcgagcggagccatctcacaaatattacctgttgttgttcacgcttg--ttcagttcattcgttggggattaaatgtatccgaagtttgtttag---

upper sequence: GRMZM2G041797_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 5'ss of exon 1

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgcccacgatctgtctctgaatgcttt-tgatttttttttgcccgtagtttcgtctcagctgatgtgcgttgttgctgcgcgtcaacgattgtgaca---
||| || || ||||||||||||||||| ||||| || || ||||||||||| ||||| || |||  ||| ||||||||||| ||  | |||||||| ||||| ||||    |   ||||   ||  | ||     ||| |   ||  |  |      | ||   |        |||   ||| |  ||     |||        
CATTCCTTCTTTCAAGATCTACCGCGGCGTCGCTGGACTTTACGACTACGGACCGCCGGGATGCGCCGTCAAGGCCAACGTCCTCGCTTTCTGGCGTCAGgt-atgcagcggcagtgtcggagatcgattcgcagtttctaactgatcaaacccatatttcgttta---caaattgggactgtgaatcttaatttgaattgcaa

upper sequence: GRMZM2G041797_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 1

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtga---tgcccacgatctgtctctgaatgcttttgatttttttttgcccgtagtttcgtctcagctgatgtgcgttgttgctgcgcgtcaacgattgtgaca
||||||||||||||||||||| || || ||||| || || |||||||| || || ||||| |||  ||| ||| |||| || ||  |||||||||| ||||| |   |  |   ||| | | |    ||  |    |        ||| | |  ||  ||   |||||      |   ||| |  || | ||  ||   |   
CATACCCTCCTTCAAGATCTATCGTGGGGTCGCCGGCCTTTACGACTATGGCCCTCCCGGTTGCGCCGTCAAGTCCAATGTTCTCGCCTTCTGGCGTCAGgttaatttttctttgatttctattactattttggaaagaaaaacatgctcctttttaggttcaagctgtaaactgaacttggtcagctttaattatatag---

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|18649594|gb|BM498413.1|BM498413

EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTAACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG

EST: gi|87152971|gb|DY397760.1|DY397760

EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTAACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG

EST: gi|33100212|gb|CF060172.1|CF060172

EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG

EST: gi|93284057|gb|EB676321.1|EB676321

EST:     CTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG
genomic: CTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG

EST: gi|18450658|gb|BM428936.1|BM428936

EST:     GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAG                         CACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTAACG
genomic: GGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACG

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: 47 (upstream exon), 48 (downstream exon)
Score: 169

CATACCCTCCTTCAAGATCTACCGCGGTGTCGCGGGGCTCTACGACTACGGGCCGCCCGGGTGCCGCGTTAAGGCCAACGTGCTTTCCTTCTGGCGCCAGgtgatgccca ... ttctccccagCACTTTGTTTTGGAAGAGAATATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTCTTGAAGGCATCGGGCCATGTCGAGAAGTTTACTGACC

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 123

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 65