ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TTCATGATGCTTTGTCGGGGCACACTTCAGCAAATGTTGAGGAGGCTATTTGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatcatcgcataattggatggtgcttcttattacttcaattcaaaaggaatgtgttgcctttcccacttccctatgaatttaatcccaatgaaatgtttttttctctcggaattctag

Basic information

species	Zea mays
transcript	GRMZM2G100872_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 3

TTCATGATGCTTTGTCGGGGCACACTTCAGCAAATGTTGAGGAGGCTATTTGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatcatcgcataat-tggatggtgcttcttattacttcaattcaaaag---gaatgtgttgcctttcccacttccctatgaatttaatcccaatgaaat---gtttttttctctcggaattctag
|||||||||| || ||||| |||||||| || |||||||| |||||| |||||||||| |||||| |||| |||||||||||||| ||||| ||||| ||||||| |||||   | ||| |  |     | | |  |||  |   || |       | |||  || ||  |   || ||  ||| || || |   | || || |   ||| | ||  |||  ||||  ||
TTCATGATGCCTTATCGGGACACACTTCTGCTAATGTTGAAGAGGCTGTTTGTTATTCAGAACATGGTGCAGTCAAATGTATTGGCATGACAATTGAGACgtaag-atcatttgacaatctaaactacccatatgcttaggttccttgatggttctgtatgatttccccatgaaacatctttattaacttcagttctataaactattgttgtctttcctcaaaattacag

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 3

TTCATGATGCTTTGTCGGGGCACACTTCAGCAAATGTTGAGGAGGCTATTTGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagt-atcatcgcataattggatggtgcttcttattacttcaattcaaaaggaatgtgttgcctttcccacttccctatgaatttaatcccaatgaaatgtttttttctctcggaattctag
|||||||||||||||| || ||||| || || ||||| || |||||| |    || || || ||| | ||   ||| |||||||||||||||||||||||||||||  | |     |       |   |   |||  | || |   ||||    | |    || || |  |  ||     | |||  ||    |||| |  ||                     
TTCATGATGCTTTGTCTGGACACACATCTGCTAATGTGGAAGAGGCTGTGGCATACTCTGAGCATGGGGCAACCAAGTGTATTGGTATGACGATTGAAACgtaagttgttaatatttgtgaaagtttggagccttggt-ctgctggtcaagtacagttacgtgtctgtttctttttttggttaataaaaa--taatgcatggt---------------------

upper sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 3

TTCATGATGCTTTGTCGGGGCACACTTCAGCAAATGTTGAGGAGGCTATTTGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagt----atcatcgcataattggatggtgcttcttattacttcaattcaaaaggaatgtgttgcctttcccacttccctatgaatttaatcccaatgaaatgtttttttctctcggaattctag
| |||||||||||||| || |||||||| || |||||||| |||||| ||   || || || ||||||||  | || |||||||| ||||| |||||||||| |||    ||   | |    |   ||||   |||  || |  |  || |  | |       |||   ||            |  ||| ||      |  ||| || |                  
TACATGATGCTTTGTCAGGACACACTTCTGCCAATGTTGAAGAGGCTGTTGCCTACTCAGAGCATAGTGCAATAAAGTGTATTGGAATGACCATTGAAACgtgagttactatttgccctctttgaaatgggaattcacatcatcttcatccctatgctgaacattggtcttagt---------tagattcaaatttcctataattttct------------------

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|76923552|gb|DV169543.1|DV169543

EST:     TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGGAAC                         GAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGG
genomic: TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGG

EST: gi|211469955|gb|FL098251.1|FL098251

EST:     TATTTCCGAAC-TAATGCTGCCAAATGT-TTGGGTATGACGATTGAAAAC                         GAGACCTGATT
genomic: TATT-CCGAACATAGTGCTGTCAAATGTATTGG-TATGACGATTGAAA-Cgtaagtatca ... ggaattctagGAGACCTGATT

EST: gi|78121954|gb|DV540338.1|DV540338

EST:     TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAAC                         GAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGG
genomic: TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGG

EST: gi|148941357|gb|EC886266.2|EC886266

EST:     TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAAC                         GAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGG
genomic: TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGG

EST: gi|149001061|gb|EE038313.2|EE038313

EST:     GTTATTCCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAAC                         GAGACCTGAATATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTA
genomic: GTTATTCC-GAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTA

EST: gi|91049795|gb|EB160213.1|EB160213

EST:     TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAAC                         GAGACCTGATTATTGCTTGGGGC
genomic: TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGC

EST: gi|148940806|gb|EC885631.2|EC885631

EST:     TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAAC                         GAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTA
genomic: TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTA

EST: gi|89253138|gb|DY624924.1|DY624924

EST:     TGTTATTCAGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAAC                         GAGACCTGATTATTGCT
genomic: TGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCT

EST: gi|78119531|gb|DV537915.1|DV537915

EST:     GTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGGATTGAA-C                         GAGATTTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATG
genomic: GTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACG-ATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATG

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), 49 (downstream exon)
Score: 124

TTCATGATGCTTTGTCGGGGCACACTTCAGCAAATGTTGAGGAGGCTATTTGTTATTCCGAACATAGTGCTGTCAAATGTATTGGTATGACGATTGAAACgtaagtatca ... ggaattctagGAGACCTGATTATTGCTTGGGGCCTCATCTGCGCCAGATGCTATCTTATGGTTGTACTCGCCTGGAAATTGGTGTCCAGAGTACATATGAAGATGTTGCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 96