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

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA

Basic information

species	Zea mays
transcript	GRMZM2G034143_T01
intron #	7
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacac-ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
                                            | |||   |        | || | ||  |||   | |  | | || ||| ||  ||       |   | || ||  | |      ||  ||   | || || ||   |||       ||||   ||   | ||  |||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || |||||||| ||||
-------------------------------------------gttacatggtcacatacctttttactcactagagctgt--ttttatttaacatgtttacaaatcttagttgt-taggtcagatctcct--tgatgattcttttttgaaattaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacac-ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
|| |||  |   | |||||| |  |||||||| | ||  |  |||               || || |||   || ||| || |   |||||  || |  |  ||||||   ||         |  ||  ||  ||   | ||||| ||   |||       ||||   |  | ||||  |||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||| || |
gtaacatggtcacatctattactgtttttgtttttcactagttct---------------gtttttatt---taacatgtttacaaaatat--tagttgttacttgttaggta--------cagacttcct--tgatgattcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaa-tataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA-
                                                                            || || ||| |  ||| |||||||| | |    |  |  |||  ||  ||||| |  |   | |   ||| || |   |  ||  || ||  || |||| |   ||||| ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||||| || || || || || ||||| ||| ||||||| | 
---------------------------------------------------------------------------aatattaatcaagctatcatattctt-tatcagagtttgatgttaat--agctaccatt---caatggatttttgtggctgatt--cttatgtaatacttgtt-gcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
                                                | | ||| |  |||  ||||| || | ||     | ||||||||   ||| | | || |||| ||   || ||||   || |||||          |||||| || |             | ||||     ||||| || |||||||| ||||| |||||||| ||||| || || || || ||||||||||||||||| || || || || ||  |||| ||| ||||||| |
-----------------------------------------------gatcttttcgtaggttatgattataaatca-----agctaatata---ttcctttttt-ttgcttaccatatattag--taactgtt----------tcttataatat-------------atacttgat-gcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactc-attcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
                                                                            | ||| |   ||  ||  ||| |    || |   ||  ||    ||||  |||||    | || |  |||  | |   |  ||  || ||  || |||| |   ||||| ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||||| || || || || || ||||| ||| ||||||| |
----------------------------------------------------------------------------aattttaatcaagctatcattttc--tttatcagattttgatggttaa--tatctaccatttaatggatttgtgttgctgatt--cttatgtaatacttgtt-gcagTATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCA

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7

gttacaaagcttc--ctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatc-attttttggctaataa-aacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
||||    |  |      | || |  | | | || | ||||||    ||||| |  | |     ||      | |   || ||    |  | | || |   ||| || ||   |  | |   ||  ||  | |    ||||    ||  || | || ||||   | ||   |||  |||    ||||||||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| |||||||| ||||| || ||||| || ||| |||| || |
gttagcccgtcttagtattgttactgtatatattat-catcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttc--tcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatag-tgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
                                                                                                        | |||  | | |||| |||    | | |      || |   | |  | || ||||      | |||| ||| |   ||||||||||| ||||| ||||| || ||||| || ||||| |||||||| ||||| || || ||||| || || || |||||||| || ||  |||| || |
-------------------------------------------------------------------------------------------------------gttttgtgtggctgtatattc--ttgttttgcaaataatttctttatttatgttttcatgtgtgaaactcttat--gcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA

upper sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7

gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
                                                                               || | || | |   || |    ||   |||| |        ||| ||    |||||| ||||   | | ||  |  |    ||  ||    |  ||    ||||||||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||| ||||| || || || || || ||||||||| |||| || |
-------------------------------------------------------------------------------tttaacttagaggttaatgcaatcagattgcttttcagtttttatgca---tgttgtatacttcctttaatgttaataatccttttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA

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|78113249|gb|DV531643.1|DV531643

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG

EST: gi|71439660|gb|DR820710.1|DR820710

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG

EST: gi|148995152|gb|EE034432.2|EE034432

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTA
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTA

EST: gi|18661324|gb|BM501354.1|BM501354

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTAAGCC
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCC

EST: gi|149020749|gb|EE045750.2|EE045750

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTAAGCCTGCTTTT
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTT

EST: gi|148943394|gb|EC888453.2|EC888453

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG

EST: gi|149088610|gb|EE177727.2|EE177727

EST:     GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAG                         TACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG
genomic: GTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAG

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: 99

ATGCCGACGTACGGTTAACAAGGAGGATCCGTCGTGATACCATTGACAAGGGTAGAGATATCAAAGCTGTGTTAGATCAGgttacaaagc ... ttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 84

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 83

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA

                               ggctaat  putative branch site (score: 83)
                                          cacttttcc  putative PPT
               attcttatcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA