ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtaccagtcaggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag

Basic information

species	Zea mays
transcript	GRMZM2G029685_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G43190.1 (Glycine max), 5'ss of exon 4

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagt-----accagtcaggaattgcta-----ctcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag
||||||||||  ||||||||||| |||||| | ||||| ||||||||  | ||||| || || ||||| || ||||| || |||||||| | |      | ||  |  | || ||      ||  | |   | |||||    || | || ||  || |    || |   ||  | ||||
AACGGCCTTGACACCAAGGTAGAAAAGTCAAGGAAGCAAATGAAGGAGAGAAAGAATAGAGCTAAGAAGATTCGTGGAGTAAAGAAGgtaattttgtagctagctataattttctttacctcttatgtgatccttgtttcattaaaattaaaacatatggcatgtattgttcgt-gcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G04920.1 (Arabidopsis thaliana), 5'ss of exon 4

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagta--ccagtcaggaat--tgcta-ctcgtattccc-attgttctggtacatttcaattatgtttgctgcacaattttttgcag
|| || ||||  || ||| | ||||||||| | || || || |||||| | ||||||||||||||||||||||||||||| ||||||||  |||  |  ||      |  ||||| ||  | ||    |||||    |||   || ||  || | |  ||  |||| ||| ||||
AATGGACTTGACACTAAGATTGAGAAGTCAAGGAAACAAATTAAGGAAAGGAAGAACAGGGCGAAGAAAATCCGTGGTGTTAAGAAGgtatgtatactggttttccctcttgctatcttctgtttttgattgtgactgta-gctttaagaatctgttttgatcaatgttt-gcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G28060.1 (Arabidopsis thaliana), 5'ss of exon 4

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgag---------taccagtcaggaattgctactcgtattcccattgttctggtacatttcaatt--atgtttgctgcacaattttttgcag----
|| || ||||  |||||| | ||||| ||| | || ||||| |||||  | ||||||||||||||||| ||||||||||| |||||||| ||          || |  ||| |||    | | |   |     ||||   |    |||    |  | | |   ||||   |||| ||       
AATGGACTTGACACCAAGATTGAGAAATCAAGGAAACAGATCAAGGAGAGGAAGAACAGGGCGAAGAAGATCCGTGGTGTTAAGAAGgtaagagagaccaacactaaccagaaatctacatttgctattgttatgtttgtgcctgttttgtcttaacgatatttgcattgttttgtgagtgtag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv07s0151g00900.t01 (Vitis vinifera), 5'ss of exon 4

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagta--------ccagtcaggaattgctact-cgtattcc--cattgttctggtacatttcaatta---tgtttgctgcacaattttttgcag---------------------------------------------------------------------------------
|| ||  | | ||||||||| || |||||| | ||||| ||||||||| | ||||||||||| |||||  |||| || ||||||||||| |  |         |  |      ||| |  |  | | ||   || |  |      | ||||||||    | ||||||| ||| |   || |                                                                                   
AATGGATTGGATACCAAGGTGGAAAAGTCAAGGAAGCAAATGAAGGAAAGGAAGAACAGGGCCAAGAAGGTCCGAGGAGTGAAGAAGgtaaagaaatcatcttccttttaaccttgttggtgtgcactctagcaatagtaccaggcctttcaatttccttttttgctgtacactgggttactattgccattcccattagccatattatttgccttcaaagatttgggaccttcacgttcattgtactactcgttactcttgcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 5'ss of exon 4

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtaccagtcaggaattgctactcgtattcccattgttctggtacatttca----attatgtttgctgcacaatttt--ttgcag--------------------------------------------------------
|| || || ||||||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||||  ||     |  || ||||          |  |||       ||  | || |     | ||||    ||   |  ||   |||  |                                                        
AATGGTCTGGCTACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGTTCGAAGAAGATCAGGGGTGTGAAGAAGgtatgttgatatgtggcattgtcttggaatgtggcatccagaaagtgaaatttacattgtcatgtaaattgtgtagcttcgattgatgcagacgagtgtgtatgtgatgaagtgtcttacaaccttcatttggcttgactgcag

upper sequence: GRMZM2G029685_T01 (Zea mays), 5'ss of exon 3
lower sequence: PP1S450_9V6.1 (Physcomitrella patens), 5'ss of exon 4

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtac-cagtca--ggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag-------------------------------------------------------------------------------------
|| ||  | || |||||||| ||||||||  | |||||||| ||||| || |||||| |  ||||||| ||| | ||||||||||||||  ||   || ||   ||||||  |   |  | |   |||    |      |||  ||||     ||| | | |      |                                                                                        
AATGGATTGGCAACCAAGGTCGAGAAGTCGAGGAAGCAGATCAAGGAGCGCAAGAACCGATCGAAGAAGATCAGGGGTGTGAAGAAGgttcgttttcattcgttggaattattgtcctaagttatattaagttcaggtcttttcattactgaagctacgctaccggaggttatcatgttttctcctgcattcttattgtgcgtttatgagtatgtttacaatgaagtgtctcacgacctgcatttgcttggtcccag

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|5761771|gb|AI966819.1|AI966819

EST:     GAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: GAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|211014258|gb|FL283800.1|FL283800

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAATTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|15079941|gb|BI388886.1|BI388886

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAATTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|211014266|gb|FL283808.1|FL283808

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAA
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAA

EST: gi|113701166|gb|EE678670.1|EE678670

EST:     AAGAACAGGGCGAAGAAAATCCGTGGTTTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|16926632|gb|BM079700.1|BM079700

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|37376305|gb|CF624665.1|CF624665

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|60397441|gb|DN230257.1|DN230257

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

EST: gi|60355885|gb|DN222858.1|DN222858

EST:     AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAG                         ACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG
genomic: AGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTG

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), 49 (downstream exon)
Score: 99

AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtacca ... ttttttgcagACAAAGGCTGGAGATGCCAAGAAGAAGTAAGGGAGGAAGTTACTTGCCTTGCTCTTTCTCTCATCATAGGCTTTGGTTTGTTTAGGGTGGGGCTCCTTCC

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 131

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 79

Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 71

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGGCCTTGCTACCAAGGTAGAGAAGTCACGAAAGCAGATGAAGGAACGTAAGAACAGGGCGAAGAAAATCCGTGGTGTGAAGAAGgtgagtaccagtcaggaattgctactcgtattcccattgttctggtacatttcaattatgtttgctgcacaattttttgcag

- - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG