ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...agttttgtgtttaaattgactaagtatgttagggtaacacggatctgtttatttttttccaatatgtgataacatttcgatttttttaaaaattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCAAGAAGAAGAAAAGCCATTTTGATAATCCTCTTGTCCCAAGCAAGAAATC

Basic information

species	Zea mays
transcript	GRMZM2G068151_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G068151_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g60700.2 (Oryza sativa), 3'ss of exon 1

agttttgtgtttaaattgactaagta-tgttagggtaacacggatctgtttatttttttccaatatgtgataacatttcgatttttttaaaaattatgcagGAATTTTCTCA-GCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCAAGAAGAAGAAAAGCCAT--TTTGATAATCCTCTTGTCCCAAGCAAGAAATC
|  ||| | ||      ||| |   | || ||   |   | ||  | | |  |||| | |   |||||| |||| |   |||  | ||  ||||| || || |  |||| |    ||| |  |||||||||||||||||||| || |||||||||||||||||    | |  | | |  |     | |    | |||||  |  
aactttttattgttgccgacgactaactgctatattgtgatggggcagctacttttgtgc---tatgtgctaac-tcaggatcctatttgaaattctgtagcagCTTTCCCTCATTGTACACATGATGGGTTGCTTCACTGTCCTGAGATCCAAGAAGAAGAAGCCTCTTGCTCTCACCAAGAAATCGGTTGATGCAAGGGAAA

upper sequence: GRMZM2G068151_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g60700.1 (Oryza sativa), 3'ss of exon 1

---agttttgtgtttaaattgactaagta-tgttagggtaacacggatctgtttatttttttccaatatgtgataacatttcgatttttttaaaaattatgcagGAATTTTCTCA-GCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCAAGAAGAAGAAAAGCCAT--TTTGATAATCCTCTTGTCCCAAGCAAGAAATC
   |  ||| | ||      ||| |   | || ||   |   | ||  | | |  |||| | |   |||||| |||| |   |||  | ||  ||||| || || |  |||| |    ||| |  |||||||||||||||||||| || |||||||||||||||||    | |  | | |  |     | |    | |||||     
gacaactttttattgttgccgacgactaactgctatattgtgatggggcagctacttttgtgc---tatgtgctaac-tcaggatcctatttgaaattctgtagCAGCTTTCCCTCATTGTACACATGATGGGTTGCTTCACTGTCCTGAGATCCAAGAAGAAGAAGCCTCTTGCTCTCACCAAGAAATCGGTTGATGCAAGGG---

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|211225792|gb|FL287046.1|FL287046

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|93282186|gb|EB674450.1|EB674450

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|71330078|gb|DR801779.1|DR801779

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|78116848|gb|DV535235.1|DV535235

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|211225789|gb|FL287043.1|FL287043

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|211225793|gb|FL287047.1|FL287047

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|211223729|gb|FL287034.1|FL287034

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|211225791|gb|FL287045.1|FL287045

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|30087714|gb|CB885920.1|CB885920

EST:     GACG-TCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCAC-GGTCTCAGATCCA
genomic: GACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|50328480|gb|CO523606.1|CO523606

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|211225787|gb|FL287041.1|FL287041

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|211223732|gb|FL287037.1|FL287037

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

EST: gi|71321873|gb|DR797626.1|DR797626

EST:     ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAG                         GAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA
genomic: ACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCA

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: 59

CCCTCCCCCGGCGTGCGCTCCCTCCTGTCTCTCTTGGCGACGACTGGGCAACGGTCGCAGCTGTATGTTCGAGCCCTTCGCCGACGACGTTCACCACCAGgtacggacgc ... aattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCAAGAAGAAGAAAAGCCATTTTGATAATCCTCTTGTCCCAAGCAAGAAATC

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 105

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 89

Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 29

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgtttatttttttccaatatgtgataacatttcgatttttttaaaaattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCAAGAAGAAGAAAAGCCATTTTGATAATCCTCTTGTCCCAAGCAAGAAATC

                     tgataac  putative branch site (score: 29)
               aatatgtgataacatt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttttgtgtttaaattgactaagtatgttagggtaacacggatctgtttatttttttccaatatgtgataacatttcgatttttttaaaaattatgcagGAATTTTCTCAGCTGTGCCAATGATGGGTTGCTTCACTGTTCTCAGATCCAAGAAGAAGAAAAGCCATTTTGATAATCCTCTTGTCCCAAGCAAGAAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - -tgtgttt