ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctctagcgatcttgagcaaaacttgggtggtgtaaggtctatggctgtgcaaattgtgatttctgatgtgatattgtacatgcag

Basic information

species	Zea mays
transcript	GRMZM2G009845_T03
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G009845_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 5'ss of exon 10

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCA---GCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctctagcgatcttgagcaaaacttgggtggtgtaaggtctatggctgtgcaaattgtgatttctgatgtga-tattgtacatgcag
   ||||||||||||||||||| || |||||  | || || |||||||||||||| |||||   ||||  ||||||||| |||||||||||||| ||||||||||||||| |||   |   || | | ||    |  ||  ||      |  || || |    || ||||    ||| | | ||||||  ||||||
---AAGATGATGCCATGCCCTCAGGTGACAACGCTCAAAACGGCTTCAACTTTGGAAACCAGCAGCCCAATGTTCCATCGGGTGGATTCAACTTTGGCTGAAGgtatgctatctttagcagttaaactaagtaggattgtggttgatcatggggatg-gtgttttctgatc---gatataaatattgtttatgcag

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|211137300|gb|FL464598.1|FL464598

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|211142696|gb|FL475568.1|FL475568

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|4775859|gb|AI664864.1|AI664864

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|78026507|gb|DV494894.1|DV494894

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|60357859|gb|DN224832.1|DN224832

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|67011792|gb|CO440541.1|CO440541

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|488236|gb|T18817.1|T18817

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTNGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGT
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGT

EST: gi|60398457|gb|DN231273.1|DN231273

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|211137299|gb|FL464597.1|FL464597

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|71322677|gb|DR798010.1|DR798010

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|211134458|gb|FL464549.1|FL464549

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|12969842|gb|BG266684.1|BG266684

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCCTTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|113701056|gb|EE678560.1|EE678560

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|78026876|gb|DV495263.1|DV495263

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|37381222|gb|CF627483.1|CF627483

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|84969435|gb|DW467872.1|DW467872

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|14245548|gb|BG874130.1|BG874130

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|37377257|gb|CF625217.1|CF625217

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|60340999|gb|DN207972.1|DN207972

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|166673354|gb|EG308254.1|EG308254

EST:     AACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: AACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

EST: gi|211175883|gb|FL475297.1|FL475297

EST:     TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAG                         ATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG
genomic: TTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGG

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: 327

AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctc ... gtacatgcagATGCCCATTTGGAATGGCGGCTGTGCCATTGTGCCTTGGCCTAGTGGTTGGGGCTAGTCAGAGTTGGGGTAGTGGCGTCGTCCTCCAAAACCTTGGTTCG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 393

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 484

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 313

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGATGATGCCATGCCCTCTGGCGACAATCCCCAGAATGGCTTCAACTTTGGGAACCAGCCCTCTGTTCCATCAGGTGGATTCAACTTCGGCTGAAGgtatgctctctagcgatcttgagcaaaacttgggtggtgtaaggtctatggctgtgcaaattgtgatttctgatgtgatattgtacatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG