ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC

Basic information

species	Zea mays
transcript	GRMZM2G409104_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G08130.1 (Glycine max), 3'ss of exon 6

gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC
                                                 ||| |    ||  |||  | |     |  |  |  |||    |  ||  |           | ||||  |  |||  |  | ||  ||  | | | | || || ||| ||||  | | ||||||||||  |||||||| ||||| ||||| ||||| || ||||| || || |||||||| |||||||||||  ||||||| || |
------------------------------------------------gttagttagttactaca--atttgtagcaattgaattacca--aagtgacac----------taagaa--ttggatttagatgttgatttct-tttttaccttgtagGCAAGTGATGTGAAGTGGGCATATCGCTGGGATACCTATCTTCTAATGGCCGATGACCAGATTCACTGGTTTTCAATTGTCAATTCCTTGATGATTGTAC

upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G36550.1 (Glycine max), 3'ss of exon 6

gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC
                                                                   |||  | ||  |       ||  |  ||         |  |  | ||||  || |||  |  | ||  ||  | | | | || || ||| ||||  | | ||||||||||  |||||||| ||||| ||||| |||||  | ||||| || || |||||||| |||||||||||  ||||||| || |
----------------------------------------------------------------gttagttactacaatttgta-gcaactgaattac-caaagtgacactaagaa--tcggatttagatgttgatttct-tttttaccttgtagGCAAGTGATGTGAAGTGGGCATATCGCTGGGATACCTATCTTCTTATGGCCAATGACCAGATTCACTGGTTTTCAATTGTCAATTCTTTGATGATTGTAC

upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 6

gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagt-tcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC
                                      || |||||  | || |  |  ||||   | |  |   |  | |||||     ||                ||  ||    | | || | | | ||  | |||| ||  ||   ||||||| |||  | | || ||||| || || ||||| ||||||||||||||||| || || ||||| || |||||||| |||||||||||  ||||||| || |
-------------------------------------gtaagacca--catactttataataaataatgattttgccattaacctgtgtgta----------------ctacaggcaatgatattcctgtattgctgtcatgtgcttggtatgcagGAGAGTGATGTGAAATGGGCCTCTCGATGGGATACCTACCTTCTGATGGCCGATGATCAAATTCACTGGTTTTCAATTGTCAATTCTTTGATGATTGTTC

upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7

-------------------------------------gttagtttcaactatttttcatcttgaa--cttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttga-----gaagttcagatgcattt---tttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC
                                          ||  |||  |||||  | || ||  ||| |     | ||| ||   | |  | |        | |      | |||||||| |   || | |    |||||   |  ||      ||  ||| |||   | |   | | ||||   |  ||||  ||||| |||||  ||||||||||||||| || ||||| || ||  |  ||||| |||||||||||||||||||||| || ||  | ||||| || ||||| || |
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacaga-tgagggtatctcgtttggatcgcgaagtgtaaacc-atgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcct-cgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC

upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ33415 (Selaginella moellendorffii), 3'ss of exon 6

gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC
                                                                                          ||  || ||  |   |  |||      ||| |      || | |       ||| ||   ||||||| ||  | |  |  ||||| || || ||||| |  |||||| ||||| |||||||||||||||| |||||||||||  |||| || || ||||| || |
-----------------------------------------------------------------------------------------gtaactgttacctgcctgtcttttatccttctg------ttctcaacgtgcctgtttgtt-tgcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC

upper sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ09669 (Selaginella moellendorffii), 3'ss of exon 6

gttagtttcaactatttttcatcttgaacttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC
                                                                                          ||  || ||  |   |  |||      ||| |      || | |       ||| ||   ||||||| ||  | |  |  ||||| || || ||||| |  |||||| ||||| |||||||||||||||| |||||||||||  |||| || || ||||| || |
-----------------------------------------------------------------------------------------gtaactgttacctgcctgtcttttatccttctg------ttctcaacgtgcctgtttgtt-tgcagGAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC

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|78110631|gb|DV529039.1|DV529039

EST:     AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAG                         GAAAGTCCCTATCA-GTGGGCATCACGCTGGGA
genomic: AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCC-TATCAAGTGGGCATCACGCTGGGA

EST: gi|211264101|gb|FK945702.1|FK945702

EST:     AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAG                         GAAAGTCCTATCAAGTGGGCGTCACGCTGGGACACCTACCTTCTGATGGCA
genomic: AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCA

EST: gi|211264100|gb|FK945701.1|FK945701

EST:     AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAG                         GAAAGTCCTATCAAGTGGGCGTCACGCTGGGACACCTACCTTCTGATGGCA
genomic: AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCA

EST: gi|149096266|gb|EE181975.2|EE181975

EST:     AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAG                         GAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTG
genomic: AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTG

EST: gi|91871094|gb|EB401239.1|EB401239

EST:     AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAG                         GAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCA
genomic: AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCA

EST: gi|31353543|gb|CD437900.1|CD437900

EST:     AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAG                         GAAAGTCCTATCAAGTGGGCGTCACGCTGGGACACCTACCTTCTGATGGCA
genomic: AAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCA

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: 48 (upstream exon), 27 (downstream exon)
Score: 14

CTGTGACCCACACTCAAGACGCCTTGTCGTAGACTCTGATTCACCTCAAGAAGTAGATGCCAACAAAGAGATCATTTTCACCTATGATATTAACTTTGAGgttagtttca ... tgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC

Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 13

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 16

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 22

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gttttttccttgagaagttcagatgcattttttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC