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

gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG

Basic information

species	Zea mays
transcript	GRMZM2G088231_T01
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 6

gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgat-accacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
||| |||| ||   ||  | |||| ||  ||    || | |  | |    || || |||||  |  |  || ||  ||| |  ||  | | | ||| | || ||||| |||||||||||||| || ||||||||||| || |||||||||||||| |||||||| |||||||||||   ||||||||||
gtaagtgacaacattgcattacaattttctgccattttcctttaga----ttcttatttgctactctcattataccctttttaatattttatactgtttacaacatgaagCCATCCATCACCTTCAGTGCTTATACCCGCACTACGAACTGTTGGAAATATTGTAACTGGAGATGACGCGCAAACTCAG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G39210.1 (Glycine max), 3'ss of exon 7

gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
    ||||  |   ||  ||  ||  |     ||   |  |  |    ||    |||| |  |     | |  |||  |  |||| || | | ||     |   | ||| || || || || || |||||||| |||||||| || |||||||| |||||||| || |||||||||||||| || |||
----gtgagtactttgcatacaaatgtggatgtgtagaaatatacgtattccagtgtt-gttctg--ctgtcaaattctaaatattat-tctact-----cttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACTGTTGGAAATATTGTTACAGGAGATGATTTGCAGACACAG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 6

gtatgtgaaaatgatgtgtaa-caacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
              || |||  |  ||||  |   ||  ||  |  |   | | | | |  ||   ||  |||||||     |||  |  ||| ||  |  |  || ||| || ||||| || || ||||| || |||||||| ||||||||||| ||||||||||||||||||||| |||| ||||||
-------------gtgagtactctgcttctcgaatatggctatgcaaaaatatat-gctcccatgtgtcattttaatgccaaatactaaatgtcctact--cttattcagGCACCCATCCCCTTCAGTGCTAATTCCTGCTCTTCGAACTGTTGGAAATATTGTCACTGGAGATGATATGCAGACTCAG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G41770.1 (Glycine max), 3'ss of exon 6

gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtt-tgcaccagtttttttaatcttgtatatgatgtgtgctgatac-cacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
                                ||| ||||  ||  |    | | | | ||||  | | |   || | |   ||   |  | |  |  ||| |   | ||| || || || || || |||||||| |||||||| || || ||||| |||||||| ||||||||||||||||| ||  ||
-------------------------------gtgagtactatgaatgcaaatatggatgtgcagaaatatacgtattgtcaaattctaaatattattctactcttcttcagGCACCCTTCCCCTTCAGTGCTTATTCCTGCTCTTCGTACCGTTGGAAATATTGTTACTGGAGATGATTTGCAGACAGAG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G29000.1 (Glycine max), 3'ss of exon 6

gtatgtgaaaatgatgtgtaa-caacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
              || |||  |  ||||      ||  ||  |  |   | | | | |  ||    |  |||||||     | |  |  ||||||  |  |  || ||| || ||||| || || ||||| || |||||||| ||||||||||| ||||||||||||||||||||| |||| || |||
-------------gtgagtactctgcttctcaaatatggctatgcaaaaatatat-gctcccat-gttcattttaatgccaaacactaaatgtgctact--cttattcagGCACCCATCCCCTTCAGTGCTAATTCCTGCTCTTCGAACTGTTGGAAATATTGTCACTGGAGATGATATGCAGACACAG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G06720.2 (Arabidopsis thaliana), 3'ss of exon 6

gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgt-gctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
                     ||    ||| || || | | |  || ||  |||    | ||| |  ||| || |      |  ||||   | |||  |   |  |  |||||||  || ||||| ||||| || |||||||| || |||||||| ||||| || |||||||||||| | ||||| |||
-------------------gtcagtaccat-tttataattcccttatttcatgtccacttcac-acatttgttgacaaataacttgataccttgctcttg--atttttagCCATCATTCTCCATCTGTGCTAATTCCTGCTCTTCGCACTGTTGGAAATATAGTTACTGGAGATGATATACAAACACAG

upper sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT4G16143.1 (Arabidopsis thaliana), 3'ss of exon 5

gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG
                      |  ||||  |    |  ||  |  ||  || |||| |     |  || | |  |  || |||| ||   |  | ||    | || || |||| ||||||||| |||||||| ||||| || || | | |||| || |||||||||||||||||| |||| || |||
-------------------gtgagtttcaaatcccatgatttcaccgtgctt-ttgtataatgaatgttatgtgttaatgaatattatcaat-tttattttgc-tgtagGCATCAATCACCATCTGTGCTTATTCCTGCCCTTCGTAGTATTGGTAACATTGTCACTGGAGATGATCTGCAGACACAG

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|32858412|gb|CD998093.1|CD998093

EST:     CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|18655265|gb|BM500070.1|BM500070

EST:     CAGTCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|32799121|gb|CD951357.1|CD951357

EST:     CGGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|67018866|gb|CO447615.1|CO447615

EST:     CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|32915771|gb|CF020583.1|CF020583

EST:     CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|32804164|gb|CD956400.1|CD956400

EST:     CGGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|32804033|gb|CD956269.1|CD956269

EST:     CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

EST: gi|18654987|gb|BM499792.1|BM499792

EST:     CAGTCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTTGTGGAGCTCCTCCT                         CCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT
genomic: CAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATAT

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: 869

ATGCATGCTGGGCCCTGTCATACTTATCTGACGGCACTAATGATAAGATCCAGGCTGTGATTGAAGCTGGTGTTTGCCCCCGGCTCGTGGAGCTTCTCCTgtatgtgaaa ... ccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 369

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 350

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 360

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG

                                     tgctgat  putative branch site (score: 360)
            tttttttaatcttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaaaatgatgtgtaacaacttcatgttgattacttcgatagtttttgttgtttgcaccagtttttttaatcttgtatatgatgtgtgctgataccacatgcagCCATCCATCACCATCGGTGCTTATACCTGCTCTACGAACTGTTGGGAATATTGTCACTGGAGATGATTTGCAAACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG