ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttccatctcatcctcatgcagttcacacatcaaattgctctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg...

Basic information

species	Zea mays
transcript	GRMZM2G044720_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g26940.1 (Oryza sativa), 5'ss of exon 2

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttccatc------tcatcctcatgcagttcacacatcaaattgctctttaggttctgcaaagg----aaatttatactaatcagttcaggcagtatttgcttgtg
||||||||||||||| |||| | || |||||||| |||||||| || || ||||| |||||||| || || ||||| ||||||||||||||||||||||||||||||||||       ||| ||| ||| | ||||  |||   |||    | ||| |   | ||       |||| |||| |  |   | ||   |||||         
ACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACGGGCAGCAACTTACTCGTAATAGGAAGTTCTTGACTGTGGTACCTGTGGTGCTgtaagttccatttccatttcaacctaatgtacttcat-catgggattttgttgtagttgtagaaagaactcaaaatgtataattgttgttacaataagtat---------

upper sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G01830.1 (Glycine max), 5'ss of exon 2

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcc---atctcatcctcatgcagttcacacatcaaattgct--ctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg
||||||| |||||||  |||||||| |||||||||||  | ||||||||  ||||||||||||| ||||| |||||| | || || || ||| |||||||||||||||    || |  |   |||   ||| | | |  ||  |     |||  |||  ||  |  |     | ||  |||  ||     |  |  ||   |   
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctctaatttgcttgccatcatgtttatatacaaaggtatctgcttctggtgatgtcataggg---tctatgaatgtgtgtgcacccttgttatata--

upper sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA16G02540.1 (Glycine max), 5'ss of exon 2

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcc---atctcatcctcatgcagttcacacatcaaattgct--ctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg
||||||| |||||||  |||||||| |||||||||||  | ||||||||  ||||||||||||||||||| |||||| | || || || ||| |||||||||||||||    || |  |   |||    || | | |  || ||     |||  |||  ||  |  |   | ||||  |||  ||     |  |  ||   |   
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGGAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttctctaatttacttgccatcatttttatatacaaagttatctgcttctggtgatgtcataggg-tctata--aatgtgtgtgcacccttgttatata--

upper sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G05940.1 (Glycine max), 5'ss of exon 2

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttccatctcatcctcatgcagt-----tcacacatcaaattgct--ctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg
||||||| |||||||  |||||||| |||||||||||  | ||||||||  ||||||||||||| ||||| |||||| | || || || ||| |||||||||||||||  ||| ||   |||||  |     | | | |  ||  |     |||   ||  ||  |  ||  | |||   | |  |     |  |  |   |     
ACCAAGGGATCTACAATAGATTGACTTGGTGGGAGCAGGTAGACAATGGAAAGCAGCTTACTCGTAACAGGAAGTTTCTCACAGTTGTTCCTTTGGTGCTgtaagttc--tctaatttgcatgccatcatttttatatacaaaggtatctgcttctagtgatgtcatagag-tctatgaaagtgtgcgtgtgt-gcgtgcaccc---

upper sequence: GRMZM2G044720_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv02s0025g02260.t01 (Vitis vinifera), 5'ss of exon 2

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttccatctcatcctcatgcagttcacacatcaaattgctctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg--
|||| || |||||||  ||  | || |||||||||||||| |||| |||  ||||||| ||||| || ||||||||| | ||||| || ||  |||||||||||||    | ||| |         ||      | |  |||    | |   |   |||  |||  |  |       | | | |     ||||  ||     
ACCAGGGTATCTACAATAGGCTAACCTGGTGGGAGCAAATAGACAGTGGGAAGCAGCTCACTCGCAATAGAAAGTTTCTCACTGTTGTGCCCTTGGTGCTgtaagtattttttcagctatgaatcttttgattttgatgttgaggctaaa--taaacaagtgaatctctttgatggaattgctgatgtaatttatttcaagt

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|211339123|gb|FL064683.1|FL064683

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTATCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|4886203|gb|AI677323.1|AI677323

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|211252164|gb|FL064672.1|FL064672

EST:     AGCAGCTTACTCGGAACAGAAAGTTTTTGACCTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCCGCACTTGACTGACTACA
genomic: AGCAGCTTACTCGGAACAGAAAGTTTTTGAC-TGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATC-GCACTTGACTGACTACA

EST: gi|78086263|gb|DV514656.1|DV514656

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|211339126|gb|FL064686.1|FL064686

EST:     GCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGGTACCTGTTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGT
genomic: GCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGG-TACCTGT-GGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGT

EST: gi|60338514|gb|DN205487.1|DN205487

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|37380052|gb|CF626807.1|CF626807

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|211252163|gb|FL064671.1|FL064671

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTATCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|211252166|gb|FL064674.1|FL064674

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|211252165|gb|FL064673.1|FL064673

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTT-GACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCAT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCAT

EST: gi|78025996|gb|DV494383.1|DV494383

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

EST: gi|149084440|gb|EE173898.2|EE173898

EST:     CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCT                         GTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT
genomic: CAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCT

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), 49 (downstream exon)
Score: 52

ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttcca ... gttcttccagGTATCTGATCGCATCGCACTTGACTGACTACAAGCAGCCGATGTTTTTCCTCAATACAATGGCAGTTTTTGTGCTAGTTGTGGCAAAATTGCCAAACATG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 85

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 78

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATGGTCAGCAGCTTACTCGGAACAGAAAGTTTTTGACTGTGGTACCTGTGGTGCTgtaagttccatctcatcctcatgcagttcacacatcaaattgctctttaggttctgcaaaggaaatttatactaatcagttcaggcagtatttgcttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggaaa