ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaatatttgtttggttgctttgaccaggcactatcataacttattgtgccctcctccaaagtcccgcttatccttggacagaaaaaaaaaatctt...

Basic information

species	Zea mays
transcript	GRMZM2G079365_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G079365_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g06170.2 (Oryza sativa), 5'ss of exon 2

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaatatttgtttgg-ttgctttgac----caggcactatcataacttattgtgccctcctccaaa-gtcccgcttatccttggacagaaaaaaaaaatctt
 |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||| |||||||||||  ||||||||||||| || ||||||   | |||   |   | |||   || |    ||   |||| |||||      |     | ||| |   |  | | | ||  || |   |   |          
GAAGGAGAGGAAGATCAAGTACACCGGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCAACCACGCTTTCAACACAGCTCACGCTGCTCCAGgtatgcattatagctcaagcttgtggtgcctctgcaactactaccataaaagtgaggctagtgctctatctgatcagttgattttttgtttggctatgct------

upper sequence: GRMZM2G079365_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G09140.1 (Glycine max), 5'ss of exon 2

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaatatttgtttggttgctttgacc---aggcactatcataacttattgtgccctcctccaaagtcccgcttatccttggacagaaaaaaaaaatctt
|||||||||||||||    ||||| |||||| ||||||||||||||||||| || ||||| || || || |  ||||| |||||||| ||  | |||||||||     | |   ||| |||  ||        | |  ||| | ||      || |    | |  |        ||| | ||||          |   |    
CAAGGAGAGGAAGATTCGTTACACAAGTGAGTTGGAGAGGAAGGTGCAGACTCTTCAGACTGAAGCAACTAACCTTTCTGCACAGCTTACCATGCTTCAGgtacatcctttccttttcgttttttgtgtttataagtcctagcttatgaagatgagtaaacatgaatttggtaacttgttcttgtcagtgtttgatggag---

upper sequence: GRMZM2G079365_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0076g00330.t01 (Vitis vinifera), 5'ss of exon 2

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaatatttgtttggttgctttgaccaggcactatcataacttattgtgccctcctccaaagtcccgcttatccttggacagaaaaaaaaaatctt---
 ||||||||||| ||    || || | ||| |||||||||||||||||||| || |||||||| || ||||| || || |||||| ||||  | || ||||||  |  |||      ||  | ||  ||  | |   | ||  || |            ||||| |  |  || |      | ||      |   ||  |   
AAAGGAGAGGAAAATACGCTATACTAATGAACTGGAGAGGAAGGTGCAGACACTTCAGACAGAAGCAACCACCCTCTCTGCACAGGTCACTATGCTACAGgtatgggctataca---ggaggattgtacatgacctgagcaagacctcaatcttttatatccaatgaacacctgaattaatgtcaatgtggatttattgtgca

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|148974699|gb|EE025506.2|EE025506

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|32797338|gb|CD949574.1|CD949574

EST:     CGCTGCAGACAGAGGCCACCACACTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTA
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTA

EST: gi|78121771|gb|DV540155.1|DV540155

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|78107383|gb|DV525801.1|DV525801

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|113704206|gb|EE681710.1|EE681710

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|71416543|gb|DR803743.1|DR803743

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|32787527|gb|CD936429.1|CD936429

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTA
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTA

EST: gi|91056252|gb|EB166670.1|EB166670

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|32832398|gb|CD972076.1|CD972076

EST:     CCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|74242434|gb|DT650348.1|DT650348

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|32800307|gb|CD952543.1|CD952543

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGATTTA
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTA

EST: gi|50332296|gb|CO527422.1|CO527422

EST:     CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|76016952|gb|DT944122.1|DT944122

EST:     GCTGCAGACAGAGGGCCACCACGCTTTGGGCACAGCTCACGCTTCTTCAG                         AGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG
genomic: GCTGCAGACAGA-GGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

EST: gi|93011791|gb|EB637311.1|EB637311

EST:     CGCTGCAGACAGAGGCCACCACGCTTTGGGCACAGCTCACGCTTCTTCAG                         AGGGACACTTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTGG
genomic: CGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTG

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), 48 (downstream exon)
Score: 36

CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaata ... tgtaatgcagAGGGACACCTCTGGTTTAACCACTGAGAACAGGGAGCTGAAACTCCGGTTGCAGGCCATGGAAGAACAAGCTAAACTTCGAGATG

Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 28

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 98

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 53

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGAGAGGAAGATCAAGTACACCAGTGAGCTGGAGAGGAAGGTGCAGACGCTGCAGACAGAGGCCACCACGCTTTCGGCACAGCTCACGCTTCTTCAGgtaacgaatatttgtttggttgctttgaccaggcactatcataacttattgtgccctcctccaaagtcccgcttatccttggacagaaaaaaaaaatctt

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaaa