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

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG

Basic information

species	Zea mays
transcript	GRMZM2G145595_T01
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaac-caatctttacgactc-taatcattgttcctgct----tttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                                                     | | |||   ||   |   |||||  |   | ||| | |||||    ||  || || | || |||| |  | || |||     ||||||  |    ||| |||||||| || || || |||||||| |||||||||||||| ||||||||||| |||||||| || ||||| ||||| ||||| ||||| |||||||||||||
------------------------------------------------------------------------------------gtattttatccatgctaaagcaactcttcatctactgt-gcttta---ggacagtaaccacattcttaataattcgtaaattaagttcctagtaaaatttacagCCACAAGCGAGAGAAAAGGCTGATAAGGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTCAAGGCAAACACGAAGGCTCTGGCTGAGAATGAAGGAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                                |   |  |||  ||  || | | | |  |  ||||||| ||  | |        ||| | |||  ||||  |       ||    || |||    || |||         |  ||||||| || || |||||||| | ||| || || || |||||| |||||||||  || || |||||||| |||||||||||||| || ||||| || |||||||
-------------------------------------------------------------tccatactcttttccct--tatattatttatacaataaaattactgcct--------ctcattcttcacttgaatt----ctcatgtgttgcgat--caaacataa-----aatcctgcagCCTCAAGCAAGGGAGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                                        ||  |   || | | | |  |  ||||||| ||  ||||||  |        |||  || |  ||  ||  ||    ||| ||    |   ||| |         ||||||| || || |||||||| ||||| ||||| || |||||| |||||||||  || || |||||||| ||||||||||||||| | || || || ||||| |
----------------------------------------------------------------tcaccccctttccccttatattatttatataataaaattactgcttgttgtc--------cttcactcg--tatgaactcatgtattatgataaaacatattat--------atgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 11

gtaagtga-gataccattct--ccaatattacattctctg------ttcaacatagttgaaatctgcttg--gtaaagttaatttga---ctagtacactttcttaagtataaaatcacaacttgttt-----ccaactcttgctttgcttggctagcaaaccaatctttacg-actctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
|||  | |  ||   ||| |     || |  ||||| |||      || |  ||   |||  |||  ||   ||   ||||| ||     | | |   ||||   |          |  |  || |||       ||   ||      |||| |   ||    |||  |   |   | | ||||           | ||||||| || || |||| ||| | ||| || || || |||||| |||||||||  || || |||||||| |||||||||||||| || ||||| || |||||||
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatca--aacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 6

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                                       | |||   ||  ||   ||||  ||| | ||    |  | ||   |   ||   | | | |  ||  || |  ||    |  || | | ||||       |   | ||||||| || || |||||||| ||||| ||||| || |||||| |||||||||  || || |||||||| ||||||||||||||| | || || || ||||| |
----------------------------------------------------------------------ttctgatctgt-taccccctta--tattatat----atatattaaaattactcattgtccctcact--catatgaactcatg-gattatgatca--aacattatatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctt--tacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                             |||   |||  |   |||||||  | | |  || | |   ||| ||          |    |||| ||       ||||||  |  |||  |   ||||      || |  |    ||   |||| || || |  || || |  || |||||||||||| || | |||||||| ||||| ||||| |||||||||||||||||||| || || ||||||||||
-------------------------------------------------------------gtagttttatatc--ctagtac-ttgtgtacagaagagggtcaaaaa--------gaagaatgctatg-------agcaaaatatgcttactgtaactccttatgttttgacattattgctagCCTCAAGCAAAAGAAAAAGGCGAGAAGGAAGGATTTAAAGTTAGTGTTGTCAAGACAAGTTTCAAGGCTAACACAAAGGCCCTAGCTGAAAATGAAGGAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgct-tttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                                                                |||  ||   ||    ||       | | |||       | |||| || |  |||| || |    | ||  ||  |||  ||  ||||| || || || ||||| ||||| || || |||||  || ||||| | |  ||||| ||||| ||||| |||||||||||||| || || ||||||||||
-----------------------------------------------------------------------------------------------gtaacctctagacactcttagtggattggtttttaaaaaattgcaatcctaa-tttatgatttcggtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtt-tccaactcttgctttgcttggctagcaaaccaa--tc--tttacgactctaatcattg--ttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                                                                         |||   |||   |    |  ||   ||||||    |   |    |  |||||||  ||  ||  ||| |   |  | | |  |   |||   |||||||||| || || ||||| || ||||| ||||| ||||||||| |||||||||  |||||  ||||||||||||||||||||| ||| || || |||||||| |
-----------------------------------------------------------------------------------------ttagtaatatggtggtgatctgaaatccaaccacagaaataaaagcttagcaaaaaaaaatcagtttccagtttgactgagagatctccactttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTGGTTTTAAGGCTAACACAAAGGTCCTAGCCGAAAATGAAGGGG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 11

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
    || |  |   ||  ||||||  ||          | || ||    ||    | ||||||  | |   ||||          |||| |   |  ||| | |     ||    | | |  | || || | || |  | || |  | |||   ||  | |  ||          ||  ||||| || || |||||||| ||||| ||||| ||||||||| ||||||||| |||||| || ||||||||||||||||||||||| ||||| ||||||||||
----gtaaatttaaatcatccaattatatgccacaatgttaatatga--gattagttcttggtggaataggtttg----------tttcctgcatgcaaattgatgctctggcagctagttctactctg-tgggttctctaaactctgtttttaac--tgaatataa-----aaattcacagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAG

upper sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 4

gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
                                           || || |  |||||      |||   ||    |  | || |   |    || | ||||  | ||         || | |   ||| |  |  |  || |   || |  ||                     |||||||||| || || ||||| || ||||| ||||| ||||||||| |||||||||  ||||| |||||||||||||||||||||||||| || || |||||||| |
------------------------------------------tatggtggtgatctg------aaatccaaccacagaaataaaagctt---agcaaaaaaaaaaaa---------aattgtcagttttccagtttgacaga--gatatccac--------------------tttttgcagCCTCAAGCAAGGGAAAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTAGTTTTAAGGCTAACACAAAGGCCCTAGCCGAAAATGAAGGGG

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|20512800|gb|BQ279999.1|BQ279999

EST:     CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAG                         CCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA
genomic: CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgaga ... gcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA

EST: gi|32830615|gb|CD970293.1|CD970293

EST:     CAGCTGCTTG-TTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAG                         CCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA
genomic: CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgaga ... gcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA

EST: gi|26456706|gb|CA828289.1|CA828289

EST:     CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAG                         CCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA
genomic: CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgaga ... gcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA

EST: gi|32830552|gb|CD970230.1|CD970230

EST:     CAGCTGCTTG-TTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAG                         CCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA
genomic: CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgaga ... gcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA

EST: gi|32831600|gb|CD971278.1|CD971278

EST:     CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAG                         CCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA
genomic: CAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgaga ... gcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTA

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), 43 (downstream exon)
Score: 91

TGTGGAGCAAATCAGTGGGAGGGACAACATTTTAAATCACCTAAGCATCCCAGCTGCTTGTTTCACTCACCCTGAGATCAGTATGGTTGGCTTGACAGAGgtaagtgaga ... gcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG

Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 38

Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 27

Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 48

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG

                            ctctaat  putative branch site (score: 48)
                                     ttgttcctgctttt  putative PPT
                 aatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgcttttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG