ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcctgatctcagtttttcctcaatattgtaaaattgtagagaacgctgtgctgattggcagaaatccattggaagactttctgcagctctatctcagcatatgggatatttctttttacctgaatttgaatggaaactttggtggcttatgtccttaagaaatacttcgcag

Basic information

species	Zea mays
transcript	GRMZM2G060896_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G060896_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcctgatctcagtttttcctcaatattgtaaaattgtagagaacgctgtgctgattggcagaaatccattggaagactttctgcagctctatctcagcatatgggatatttctttttacctgaatttgaatggaaactttggtggcttatgtccttaagaaatact---tcgcag
||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||| || |||||| |    |   |     |||||  || ||    || |  || |   ||| || |  |||  | |   ||   ||||    | | |||  |  | | | ||  | |        ||| |  |||| |  ||   ||     | ||||||  || |||| |||  ||  |||    |  |||
TGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTTGCTCAATTCCATCCCCAAAGAAAgtaaggactccattt---attttttttccat----tagaggtgaaattaacacttt--tgacagactcgaa---attg----attgtcttaaattat-tttcttcct--------tttatccttacttctatagaaaattttagtttggtcactaatgttctttggacctaccaaatttcag

upper sequence: GRMZM2G060896_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G41600.1 (Glycine max), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtat-gcctcctgatctcagtttttcctcaatattgtaaaattgtagagaacgctgtgctgattggcagaaatccattggaagactttctgcagctctatctcagcatatgggatatttctttttacctgaatttgaatggaaactttggtggcttatgtccttaagaaatacttcgcag
||| |||||||| || ||||| |||||||| |||||||||||||| |||||||| |||||  |||| || || || || |||||||  ||||| ||||  |||  |||   |||||| |   |||      | || | |  || ||          |  ||| || |  | |   |    | || || || ||| |  |  | |  |     | || |                                                              
TGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCTGTTCAATTCAGTCCCCCAAAACTgtaaagccatttgatctgatgatttt-----tgttctgagcttata----------ttatgactgtcgaata---aaaaaatgaattgcttcagtttcaatttaaaagtattgttact--------------------------------------------------------------

upper sequence: GRMZM2G060896_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G13210.2 (Glycine max), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtat-gcctcctgatctca--gtttttcctcaa----tattgtaaaattgtagagaacgctgtgctgattggcagaaatccattggaagactttctgcagctctatctcagcatatgggatatttctttttacctgaatttgaatggaaactttggtggcttatgtccttaagaaatacttcgcag
||| |||||||| || ||||| |||||||| | |||||||||||| |||||||| |||||  |||| || || || || |||||||  || || ||||| |||  | |   |||||  |   |||| | ||      |||  ||  | |||  |  |     |  | || |    |  | || |  || | | |     | ||                                                                                   
TGTACTTGATGGAATAGTTCAATTGACTGAGAGGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCTGTTCAATTCATTCGCCCAAAAATgtaaagtcatttgatccgatgattttgcttctgagcttatgttatgactgtcaaataaaaaatattaatcgcttcagtttcaatttaaaagtat----ggttcc----------------------------------------------------------------------------------

upper sequence: GRMZM2G060896_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 5

TGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcctgatctcagtttttcctcaatattgtaaaattgtagagaacgctgtgctga-ttggcagaaatccattggaagactttctgcagctctatctcagcatatgggatatttctttttacctgaatttgaatggaaactttggtggcttatgtccttaagaaatacttcgcag
|||||||||||| |||||||||||||  || || ||||||||||| || ||||| |||||| ||||||| || ||||| ||||||  |||||| || | ||||      ||  |  ||    ||      |  |   |  ||||  |        |  ||| ||||   | |||  |   |  ||  | |  |  | |  |                                                                               
TGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTTGTTCAATTGAATCCCCCAAGAGAgtaatttcactatttccaagcattggagttttattccatgttgtcaatgttctccttttgacttggattatatctttctcacaaccatttttaatt-tgcc-------------------------------------------------------------------------------

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|211229918|gb|FL287074.1|FL287074

EST:     AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAA                         GTTTTGGTTATTGGTGGTGGTGAATGGAGGTGTACTTCGAGAGGTATCCAG
genomic: AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGA-TGGAGGTGTACTTCGAGAGGTATCCAG

EST: gi|148991840|gb|EE033431.2|EE033431

EST:     AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAA                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG
genomic: AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG

EST: gi|71305271|gb|DR788769.1|DR788769

EST:     AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAA                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG
genomic: AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG

EST: gi|6918561|gb|AW400091.1|AW400091

EST:     AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAA                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG
genomic: AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG

EST: gi|148946476|gb|EC891786.2|EC891786

EST:     AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAA                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG
genomic: AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG

EST: gi|74240569|gb|DT648483.1|DT648483

EST:     AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAA                         GTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG
genomic: AGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGG

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: 91

TGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTTGCTCAATTCCATCCCCTAAAAAAgtatgcctcc ... tacttcgcagGTTTTGGTTATTGGTGGTGGTGATGGAGGTGTACTTCGAGAGGTATCCAGGCATAGTTCAGTGGAGTCCATTGACATATGTGAGATTGATCAGCTGGTTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126