ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctccttatccttgctttttcccaatattgtgaatatcatagacaggctgtgttgcttaacataaatcgattcacacggaatatttctttttacctgcacttgcatggaaactgtagcatgctagcaacttatattattaggaactactttgcag

Basic information

species	Zea mays
transcript	GRMZM2G120578_T01
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctccttatccttgctttttcccaatattgtgaatatcatagacaggctgtgttg-cttaacataaatcgattcacacggaatatttctttttacctgcacttgcatggaaactgtagcatgctagcaacttatattattaggaactact---ttgcag
||| |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| || || || |||||||||||||| || || ||| |   |   ||   |  |||||||    |||     |   ||  |||   |     | ||  | ||  || |  | | |     |  ||| ||||| |   ||||  || |||| | |   |   | |  ||| || || || ||| ||||    || |||
TGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTTGCTCAATTCCATCCCCAAAGAAAgta-aggactccatttattttttttcc----attagaggtgaaattaacacttttgacagactcgaaattgattgtcttaaattattttcttccttttatccttacttctatagaaaattt--tagtttggtcactaatgttctttggacctaccaaatttcag

upper sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA04G41600.1 (Glycine max), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcctt---------atccttgctttttcccaatattgtgaatatcata-gacaggctgtgttgcttaacataaatcgattcacacggaatatttctttttacctgcacttgcatggaaactgtagcatgctagcaacttatattattaggaactactttgcag
||| |||||||| || |||||||||||||| |||||||||||||| |||||||| |||||  |||| || || |||||||||||||  ||||| ||||  ||| | |   ||         ||  ||| | |   |  ||||| ||| | ||  |  | |   ||  |||||| |  |   || ||| | | | | | || ||                                                                   
TGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCTGTTCAATTCAGTCCCCCAAAACTgtaaagccatttgatctgatgatttttgttctgagcttatattatgactgtcgaataaaaaaatgaattgcttcagtt---tcaatttaaaagtattgttact-------------------------------------------------------------------

upper sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G13210.2 (Glycine max), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctccttatccttgctttttcccaatattgtgaatatcatagacaggctgtgttgcttaacataaatcgattcacacggaatatttctttttacctgcacttgcatggaaactgtagcatgctagcaacttatattattaggaactactttgcag
||| |||||||| || |||||||||||||| | |||||||||||| |||||||| |||||  |||| || || |||||||||||||  || || ||||| ||| |     ||   |      |||  |      |   || | || ||| | |     |    || || ||||| ||||     ||| |     | |   | |                                                         
TGTACTTGATGGAATAGTTCAATTGACTGAGAGGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCTGTTCAATTCATTCGCCCAAAAATgtaaagtcatttgatccgatgattttgcttctgagcttatgttat-gactgtcaaa--taaaaaatattaatcgcttcagtttcaatttaaaagtatggttcc---------------------------------------------------------

upper sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctccttatccttgctttttcccaatattgtgaatatcatagacaggctgtgttgcttaacataaatcgattcacacggaatatttctttttacctgcacttgcatggaaactgtagcatgctagcaacttatattattaggaactactttgcag
|||||||||||| |||||||| ||||  || || ||||||||||| || ||||| |||||| ||||||| || || |||||||||  |||||| || |  ||| || ||  |||         |||| |  |||| || | | ||       |  ||||| | ||  |    |  || ||  ||| ||| |||||   |   ||      |  ||  ||                                         
TGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTTGTTCAATTGAATCCCCCAAGAGAgta-atttcactat---------ttccaagcattg-gagttttatt------ccatgttg-tcaatgttctccttttgacttggattatatcttt---ctcacaaccatttttaatttgcc---------------------------------------

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|211320667|gb|FL013191.1|FL013191

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTTAATTC-ATTCCCTAAAAAG                         GTTTGGGTTAT-GGTGG
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGG

EST: gi|32919151|gb|CF023963.1|CF023963

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

EST: gi|148956445|gb|EC902269.2|EC902269

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

EST: gi|78117805|gb|DV536192.1|DV536192

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

EST: gi|148931937|gb|EC875166.2|EC875166

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

EST: gi|148930370|gb|EE284813.2|EE284813

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

EST: gi|211322828|gb|FL013194.1|FL013194

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTG-TTATTGGTG
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTG

EST: gi|149072878|gb|EE161134.2|EE161134

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

EST: gi|211322829|gb|FL013195.1|FL013195

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGGGGAATGGAAGTGTACTNCGAGAGATTTTCA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTG-A-TGGAGGTGTACTTCGAGAGATTTCCA

EST: gi|32865849|gb|CF005531.1|CF005531

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAG
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAG

EST: gi|28188224|gb|CB179834.1|CB179834

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAG
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAG

EST: gi|148963955|gb|EE015081.2|EE015081

EST:     AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAG                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA
genomic: AGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGA

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: 124

TGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCTGTTCAATTCCATCCCCTAAAAAGgtatatctcc ... tactttgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGATTTCCAGACACAGTTCAGTGGAGTCTATTGACATATGTGAAATTGATCAGCTGGTTA

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 156

Block sizes: 37 (upstream exon), 48 (downstream exon)
Score: 69