ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC

Basic information

species	Zea mays
transcript	GRMZM2G152686_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 9

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
                                     |||  | | ||     | |         | |  |  || | |  |||| ||||| ||  |||| ||||||||||||| |||||||| |||||||| ||||||||| ||||||||||||| || || ||| |||||||||| ||||||||||| ||||| |||||||||||||| |
--------------------------------gtctgaactctgaactgccatgatacccctgtgccttttcctcattcaattcccttttctaattacatttctttctgtagAATCACATGAGTGAAATGTTTGCATACCATTCAACAATGATGTCCAACACTCTTGGAACATCAATTGTGGTTTTCACCAGGACAGGATTTATGGCTATCC

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 9

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
          ||      ||||  | || |  |   | || ||    |  ||| | | ||    |  | ||| |  | ||     |  |   |      |     | |||||||||||||||| || ||||| || ||||||||||| |||||||| ||||||||| |||| ||||  || || ||||||||  | || || |||||||| |
---------gtttgaaatttaa--actcaatgactctgacttttttttaatcattgtgttctagttttactgttggtactg----aaatgtgattttttttgtactgtgtagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTTGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 9

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttc-agtttttttccatcatgctgatcttccttttccattttccaaccacatatct-ttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
                  ||    |||  |    ||||||  | || | ||  | |  || |     |   |  | ||  |  |  | | |         | | |  | | |||||||||||||| || ||||| || ||||||||||| |||||||| ||||||||  |||| ||||  || || ||||||||  | || || |||||||| |
-----------------gtttgaaatttaaactcaataactctgactttttttaatcattgtgttctactttactgttggtactgaaatgtaattttttttttgtactatatagAACCACATGAGTGAGATGTTTGCTTACCATGCAACCATGATGTCTAATACCCTCGGAACCTCAACTGTTGTCTTCACTAGATCAGGCTTCATGGCTATCC

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 9

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagttttt--ttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
||||    || ||   |  |    ||    ||    |   ||   ||| | || ||| |  ||  ||  | |||| ||    |||  |||||         |   |   |||||||||||||||| || ||||| |||||||||||||| |||||||| || |||||| |||| ||||  || || |||||||| ||||| || |||||| | |
gtttaagtcaatctatttgttgccatgtt-gactttttgtataatcctttgcactttctcatttaattgt-ctgacctgaaatttgtattttttt------ttgttcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACCCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 9

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatca--tgct-gatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
||||    || ||   |  |    ||       |  |   ||| | | |||     ||  ||  | |  || | |||||    |||  |||||          || |   |||||||||||||||| || ||||| |||||||||||||| |||||||| || || ||| |||| ||||  || || |||||||| ||||| || |||||| | |
gtttaagtcactctatttgttgccatgtt---gactttttatttaaccctttgcacttcctcatttaattgttagatctgaaatttgtattttatttttttggat-tcaatgtagAACCACATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCTAACACTCTTGGAACCTCAACTGTTGTCTTCACTAGAACGGGTTTCATGGCTGTCC

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 9

gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
||  |||||       |     || ||  |       | |||| |     |  ||| | |      |  |  |  |  |     ||||||    | |         ||  ||||||| ||||| || ||||| |||||||||||||| ||||||||||| || ||| |||| ||||  || || ||||| || || || || ||||| ||| 
gtaagccacgcctgatttccttgtcttgaaactctgcaccattgagtctatttgttatct------aatccaaaataacaagaacatttttttgcta---------ctacagAACCATATGAGTGAGATGTTTGCATACCATGCAACCATGATGTCAAACACACTTGGAACTTCAACTGTTGTCTTCACCAGAACCGGTTTCATGGCCATAT

upper sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 9

--------------------------------------gtttgccacattcacctcttaagtattcgagaaaaataacattcacctcttcagtttttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC
                                       || |||   ||    |  |     ||    ||||| ||  || |  | |  | |   |||  |   |||| |   |   |    |   |       |   | | |||||||||||| |||||||||||||| || | ||||||||| |||||||| ||||| ||  | || |||||||| ||||||||||| || || || |||||||| |
gtcatttaacatatcctttatatttattttaatgctgcattggccttgtttttgtaatgtaattttttaaaaaaaaaagtttaaatttgtactccattttaac--tgctaacaatgaatacttaccataagcttcc---tttctctgtagAACCATATGAGCGAAATGTTTGCTTTCCATGCAACCATGATGTCCAATACTCTCAGTACTTCAATAGTTGTTTTCACTAGAACTGGTTTCATGGCTATCC

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|78023476|gb|DV491863.1|DV491863

EST:     CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCGACAATGATGTCAAATACC
genomic: CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|60346042|gb|DN213015.1|DN213015

EST:     AAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC
genomic: AAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|5499208|gb|AI855075.1|AI855075

EST:     TTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCGACAATGATGTCAAATACC
genomic: TTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|213173762|gb|FM184221.1|FM184221

EST:     CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATATCATGCAACAATGATGTCAAATACC
genomic: CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|148934385|gb|EC878415.2|EC878415

EST:     TGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC
genomic: TGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|6020916|gb|AW065844.1|AW065844

EST:     CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCGACAATGATGTCAAATACC
genomic: CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|78125189|gb|DV543573.1|DV543573

EST:     GTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC
genomic: GTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|14204276|gb|BG837953.1|BG837953

EST:     CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC
genomic: CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

EST: gi|211384112|gb|FL133262.1|FL133262

EST:     CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAG                         AACCACATGAGCGAAATGTTCGCATACCATGCGACAATGATGTCAAATACC
genomic: CAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACC

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), 48 (downstream exon)
Score: 302

TCCCTTGAAAGCTGTTAAGGTCATGCACACTGTTGCCCTGAGAACCGAGGCAACTATTCCTGGTGGGGAAACACCTGCAGACCTTGGTCAGGCTTTCAAGgtttgccaca ... ctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 248

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 191

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 438

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttccatcatgctgatcttccttttccattttccaaccacatatctttctgtagAACCACATGAGCGAAATGTTCGCATACCATGCAACAATGATGTCAAATACCCTTCGAACATCAATAGTGGTTTTCACTAGGACGGGATTTATGGCTATAC