ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttcactttctcctttactttatactatcaatatttcttcaacttatacaccatcagtaccaaaaaaaaaatcttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatag

Basic information

species	Zea mays
transcript	GRMZM2G139374_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 5'ss of exon 2

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttcactttctcctttactttatactatcaatatttcttcaacttatacaccatcagtac-caaaaaaaaaatcttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatag
 ||||||||||||||  | ||||||||||||||||||||| | || || ||||| || |||||| ||||||||||||||||||||||||| ||||| |||||||||   | ||    |   |  | | |   ||||  ||||||           | |||   ||| || |   |  ||||| |   || |   |||||                                    
GTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCCTTGATTTCAAAGAATGGGAAAGCGAGGCTGAATATGAATATgtaagtccccgctgcagctgcttttgtttgtaatcagcatttctg----------atcattgatacacatatgcatgatcttttaccttaa---catag------------------------------------

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G45930.1 (Glycine max), 5'ss of exon 2

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttcactttctcctttactttatactatcaatatttcttcaacttatacaccatcagtacc--aaaaaaaaaatcttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatag
 ||||| || || ||  | || ||||||||||| || || ||||  || ||||| || ||||| |||||||| |||||| |  | |||||||| |||||||||||||  ||  ||    | | || || ||| ||| ||       |    | |  |  ||| |||   ||| | | | | || |||     |||| || |   |    | |                        
TTTTGCCACCCCTTATCGTGTAACATGGGATTATTATTTCCTGGCCCGGGAGCATACGCTTGAGATCAAAGAGTGGGAAGGGAAAGCTGAGTACGAGTATgtaagtgaccatctt----tcttctgtacactgtcacta-------agtagagaggctgtcaatacttgaaacacacatttttgttttggagatccttaccctctttgcaatcag---------------------

upper sequence: GRMZM2G139374_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G02820.1 (Glycine max), 5'ss of exon 2

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttca-ctttctcctttactttat-act-atcaatatttcttcaacttatacaccatcagtaccaaaaaaaaaatcttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatag
 ||||| |  || ||  | || ||||||||||| || || ||||  || ||||| || ||||| |||||||| |||||| |  | ||||||||||||||||||||||  || |||||| || |||  | | ||| |  |   ||| || ||  |  | ||   || |          | |||    |||  |  |    |                                     
TTTTGCCAGCCCTTATCGTGTGACATGGGATTATTATTTCCTGGCCCGGGAGCATACGCTTGAGATCAAAGAGTGGGAAGGGAAAGCTGAGTATGAGTATgtaagtgaccatctttcttctgtacactgtcactgagtagagtttgttgaaacttgaaacacacatttttgttttggagatc---cttaccctctttgcaatcag--------------------------------

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|110202367|gb|EC884264.1|EC884264

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|211004797|gb|FL233607.1|FL233607

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGATGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCCAT-TTCCTCATGCCATCTGGAACAATTGG
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCC-ATCTTCCTCATGCCATCTGGAACAATTGG

EST: gi|148931314|gb|EC874175.2|EC874175

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|93284093|gb|EB676357.1|EB676357

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|148955706|gb|EC901392.2|EC901392

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|76011882|gb|DT939052.1|DT939052

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|149110172|gb|EE293987.2|EE293987

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|74235211|gb|DT643125.1|DT643125

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|32823063|gb|CD962772.1|CD962772

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|148965948|gb|EE016864.2|EE016864

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|149079827|gb|EE168827.2|EE168827

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|148946744|gb|EC892010.2|EC892010

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|148967020|gb|EE018178.2|EE018178

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

EST: gi|71311670|gb|DR792243.1|DR792243

EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

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: 163

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 410

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttcactttctcctttactttatactatcaatatttcttcaacttatacaccatcagtaccaaaaaaaaaatcttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA