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

...ttactgcattgctatttctctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG

Basic information

species	Zea mays
transcript	GRMZM2G133082_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 3

ttactgcattgctatttctctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcata-------tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
    |    |  |||||     |  |||||| || |||| ||  |   | |  ||| |   | |  |  |||   | || ||| || |||       |||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||| | ||||| || ||  |  
----tcatctattattttctacacttagcttatc-aaataaatagaagtat--taacttgttctgtcatagattttcttttaatattatagtcttgatcctttccagCAAAGGTCTGCTACAAAAGTGACATTTCCACTTGTCTGGACAAACACTTGCTGTAGCCACCCTCTATACCGCGAGTCCGAGCTCATTGAAGATAAAAGCC

upper sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 3

ttactgcattgctatttct-ctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
||  || |    | | | |  |  |   |  | |  || ||   |  |  |   | | | || |          || ||| |    || | |    |  ||||| | ||||||||||| || || || || ||||| |||||||||||||| |||||||||||||| ||||| || || ||| | ||||| || |||    
ttggtgaaaaattctctatgttgcatgtgtattttcaagtctttgactcgtgttttaatttggtctgtttgactgagattctttgttc-tttatgatgaagCAACGATCTGCAACAAAGGTAACTTTCCCTCTTGTGTGGACAAACACCTGTTGTAGCCATCCTCTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCC

upper sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 3

ttactgcattgctatttctctaaacta-gcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-
 |  || |    | | | | ||   |  |  | |  |  ||   |  |  | | | | | || |  |       || |||      || | |    |  ||||| | |||||||| || || ||||| || ||||| |||||||||||||| || |||||||| || ||||| || || ||| | ||||| || |||     
-tggtggaaatttctctatgtatcatgtgtattttcatgtcttggactcgtgctttaatttggtctctttgactgagattccttgttc-tttatgatgaagcAACGATCTGCAACCAAGGTAACATTCCCTCTTGTGTGGACAAACACCTGTTGCAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCT

upper sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0206g00020.t01 (Vitis vinifera), 3'ss of exon 1

---------ttactgcattgctatttctctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCA--GAGTTGATTGAGGAAAATTGTG
          |   | |  |||   | |  |  || |   || | | ||||  |   | |  |   | | | |         ||   || | |   | | |   | |||| |   |||  | |   | | | || |  | |  |  | |    |      ||  |  || ||    |  |  ||  |  | ||  | |  | |    ||  
tttcggaggctgacg-agggcttactttgcagtcttggaggtttcactcaacagccgtgttattcttttatatt--------gaatctggatacaaacacctgctgcagCCATCCTCTTTACCGTGAATCAGATCTT-ATTAATGAGAATGTGCTTGGAGTGCGGA-ATGCTGCACAAAGAAAGCTATTGGGTGAACTCGGCATTCCTGCT

upper sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 3

ttactgcattgctatttctctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatccttt--acagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG-
||  | ||     |||     ||  ||     |       |||    |   ||  | | ||   | | ||     | || |     ||| |   ||  ||||||||||||||| ||||| |||||||| ||  | || ||||||||||||||||| ||||||||||| ||||| || |||||| | ||||| || ||| | | 
ttgtttcaccctgattctatcaagatatagcattctttgtaaacatca--gccagaatttgagaatcacatgctgtgttctttctgcatgtttcttgtacagCAAAGGTCTGCCACAAAGGTGACATTCCCTTTGGTGTGGACAAACACCTGCTGCAGCCATCCTCTTTACCGTGAATCAGAGCTTATTGATGAGAAT-GCGC

upper sequence: GRMZM2G133082_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S28_399V6.1 (Physcomitrella patens), 3'ss of exon 3

ttactgcat-tgctatttctctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgt--aaaatcatatcct-ttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG
  || |  | || |       |  | |||   ||  |  |  | || | | ||||   |  |      | | || || || |  |   | ||||  | || ||| || | || || || |||||||| ||||||||||| ||||| ||||| || || |||||||| || ||||| ||||| ||  | |||||||| || |   
ccaccgtgtatggttagagattggattagtgagtg-acttgcagggatgtctcct---ttagacccatggacaaaatcttatttatgttgatattatatttcagAAACGTTCGGCTACGAAAGTGACCTTTCCACTTGTGTGGACCAACACTTGTTGCAGCCATCCACTGTACCGTGAGTCTGAACTTATTGAGGATAAATACC

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|211304673|gb|FL135311.1|FL135311

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|26557862|gb|CA830097.1|CA830097

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|67022742|gb|CO451491.1|CO451491

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|15312900|gb|BI478457.1|BI478457

EST:     GAGC-TTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|154130380|gb|EC872179.2|EC872179

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|211036240|gb|FL120750.1|FL120750

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGAC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGAC

EST: gi|154130466|gb|EC872180.2|EC872180

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|37421690|gb|CF648546.1|CF648546

EST:     GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|21843201|gb|BQ703782.1|BQ703782

EST:     GAGCTTTCAGGGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTACAG                         CAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC
genomic: GAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGC

EST: gi|211304672|gb|FL135310.1|FL135310

EST:     AGCTTTCAGTGTTTTCCCTTTTCAACTCCAAATATGAGTTGCTACTGCAG                         CAAAGGTCTGCAACAAAGGTGACATTTTCCACTTGTCTGGACAAACACCTG
genomic: AGCTTTCAGTGTTTTCC-TTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTT-CCACTTGTCTGGACAAACACCTG

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: 66

GCCATCTCATGGAGAAGATAGAAGCTGGAAATGCCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAGTTGCTACTGCAGgtattcacac ... tcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG

                                           tatccttt  CT-rich tract
                             atattgtaaaatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactgcattgctatttctctaaactagcttgtctaaatcaaagggtatttcctaagtctgtttaccgcagaagatattgtaaaatcatatcctttacagCAAAGGTCTGCAACAAAAGTGACATTTCCACTTGTCTGGACAAACACCTGCTGTAGCCATCCTCTCTACCGCGAGTCAGAGTTGATTGAGGAAAATTGTG

- -ctgcatt
- - - - - - - - - - - - - - - - - - aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcagaag