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

...tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG

Basic information

species	Zea mays
transcript	GRMZM2G082484_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 1

tgtcattccttgtgctattgcacaaatcgt-ttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
|||  ||  | |    | ||   |  ||   || ||| | |  |   |    | | |||||| |||||   || |     | | || |||| |          ||||||||| |||| ||||||||||||| ||||||||||||||||||| ||||||||||||||||| ||||||||||||
tgtt-tttgtaggatgaatgtttagttcaagttacatttttctgtattaatctat-agtctttgtaaacactgttttgaatgatttattttgtgtta------tgcagATCAGTTAAAATAAATGGCTGACGCAGAGGACATTCAGCCCCTTGTCTGTGACAATGGAACCGGAATGGTCAAG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1

tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
         |   |  |   | ||||  || || |  |    | | | ||  |   |||| | | ||  ||| |  |  | ||  ||| | |  ||||  | || || |   | ||   ||||||||||  | ||||| ||||| ||||| || ||||||||||||||||||||||| |||
---agagtttgaagtaaaccctcaaa--gtctgtaaatggctgggttctgtagattgtct-attcaaacttggtggtactgacaatttat-tgtatgcgtactgtagTTTGGTAAA---AAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 1

tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaa--tgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
| |      |     || |   ||||  || || | ||    | | | ||  |   ||||    |||  ||||  |  ||| || || || ||| ||| |||     || |   | ||   | ||||||||  | ||||| ||||| ||||| |||||||||||||||||||||||||| |||
tatagaaaataaacgtaatcttcaaa--gtctgtaagtggctgggttctgcagattgtctattcaaacttgttaatactggcaatttgttctatgcatacag-

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.1 (Glycine max), 3'ss of exon 1

tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaa--tgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
 |  | |    ||  | ||   ||||  || || | ||    | | | ||  |   ||||    |||  ||||  |  ||| || || || ||| ||| |||     || |   | ||   | ||||||||  | ||||| ||||| ||||| |||||||||||||||||||||||||| |||
agaaaataaacgtaatctt---caaa--gtctgtaagtggctgggttctgcagattgtctattcaaacttgttaatactggcaatttgttctatgcatacag----tagTTTGGTAAA---AGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 1

tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattc-atgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
     ||| ||| ||| |   |      | || || |  |||    |    |  || | ||  ||  |  ||  ||   ||  |  |   |  | ||||    || || |   ||   | | ||||| ||  | ||||| ||||| ||||| || || ||||||||||||||||||||||||
----cttcgttg-gctgt-aaatgtcctggtttcacgggttgtccatacaata-caattttgttacttactga-cactttacttcatggcaccctatgctttctgtagGT---TTGTAAAAGATGGCAGATGCCGAGGATATTCAACCCCTTGTTTGCGACAATGGAACTGGAATGGTCAAG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G32220.2 (Glycine max), 3'ss of exon 1

-tgtcattccttgtgcta-ttgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
 |  |  |   |||  |  || |||   | |||   ||        | ||     | | |    |  | |||   |||||| | | |         ||||   ||||||    |||   | | ||||| ||  | ||||| ||||| ||||| || |||||||||||||||||||||||||||
ttagctgtaaatgtcttggtttcacgggttgttcatataatacaatgtttatactttacttactgacactgtatttcatggcaccct---------atgctttttgcag-

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 1

tgtcattccttgtgctattgc-acaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAAC-ATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
                |  ||  | |||| |    |   | | | | | || | ||    ||| |  |||  ||| ||   || |  |||   |  | ||  || |   |  ||||   | ||||||| ||    ||||| |||||||| || |||||||||||||||||||||||||| |||
------------aataaacgctgctaatcttcgaaactaagttgtgatctgat-tcgtgtttacttcatga-gcttatc-caattcatttcggt--ttcattttactttttttttagTGAAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 2

--tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG
   |  |||   ||    |    | ||   |  |   |||   | |||       | |   ||  || |  |||  |   | |  |  | ||  |||||||| |   | |             ||||| ||  | || || || |||||||| |||||||||||||||||||||||||| |||
atggaaattatctgaaaaagctaaaaaggtgaatatttgtcaagcagcaa-aacttaaactttgttatactttgtcccctg-acttcatatttctcatgcagGTAATAAAA----------GGATGGCCGATACTGAAGATATCCAGCCCCTCGTCTGTGACAATGGAACTGGAATGGTGAAG

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|211242790|gb|FL158546.1|FL158546

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACA

EST: gi|211245028|gb|FL158560.1|FL158560

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242796|gb|FL158552.1|FL158552

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAK                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211245027|gb|FL158559.1|FL158559

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242792|gb|FL158548.1|FL158548

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242797|gb|FL158553.1|FL158553

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242798|gb|FL158554.1|FL158554

EST:     CTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAN                         MTTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: CTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211245029|gb|FL158561.1|FL158561

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211240566|gb|FL158540.1|FL158540

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242789|gb|FL158545.1|FL158545

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242795|gb|FL158551.1|FL158551

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211245025|gb|FL158557.1|FL158557

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCSTMCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242785|gb|FL158541.1|FL158541

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211245026|gb|FL158558.1|FL158558

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|32938011|gb|CF042830.1|CF042830

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTG
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|31355598|gb|CD439955.1|CD439955

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242787|gb|FL158543.1|FL158543

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCSTCCTCCCCGTCACAK                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211245024|gb|FL158556.1|FL158556

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211245030|gb|FL158562.1|FL158562

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242791|gb|FL158547.1|FL158547

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|78083306|gb|DV511699.1|DV511699

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

EST: gi|211242788|gb|FL158544.1|FL158544

EST:     TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAG                         ATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA
genomic: TCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTA

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), 48 (downstream exon)
Score: 82

TATATCTCGCGCCTCTCGCCTTCCACTCTTTCTATACCCGCCCGCTCGCCTCCCTGGTACGCTTCGTGCCGCCGCCGCAACCTCCTCCTCCCCGTCACAGgtgagcgaat ... attcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 174

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 212

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 53

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG

                               tggtaac  putative branch site (score: 53)
                                     ctttttttattcat  CT-rich tract
                                  taactttttttattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcattccttgtgctattgcacaaatcgtttgcatgtattggagctttggtgtcagtcttagtaaatgttgctcatggtaactttttttattcatgcagATTGCAGATCATTTAACATAAATGGCTGACTCAGAGGACATTCAGCCCCTAGTCTGTGACAATGGAACTGGAATGGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- -cattcct
- - - - - tgtgcta
- - - - - - - - -ttgcaca
- - - - - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - tggagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct