ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

Basic information

species	Glycine max
transcript	GLYMA07G40170.1
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1

tgtccttcataatctcccaaataggaagaacc-caagagaatgattttt-tgaagtgttatttgcaatgtgttttattaacatta----tgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
       ||   | ||     || ||   |   | |    || | ||   ||||    | |    ||   | || ||   | |      | || ||  | ||| |||||| |||||||||||| |||||||  |||| ||||| |||||||||||||| ||||||| |||||| || ||||| || ||||| || |||||  | ||
------ccaatgtttcttggctacgatttatttcgattatataacttccatgaaaaaatttccagaaaacgattgatatgcttctgaattattgtttacattgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g34640.1 (Oryza sativa), 3'ss of exon 2

tgtccttcataatctcccaaataggaagaacccaagagaatgattttttg-aagtgttatttgca-atgtgttttat-taacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
| || ||| |  |||  |      | |||  |     |  |  |   |   ||||| |    | | ||   | |||| |  |      ||  | || ||     ||| |||||||| ||||| || |||||||  || ||||||||||||||||| |  ||||||| ||||||||| ||||| ||  | ||||| ||||| |||||
tttctttctttgtcttgc------gtagattctgcttgccttttgcataacaagtgctgcccggacataactcttatgtgtctactaattcctttcattcgaacagAAAAGGAGAACTTGTGCCTTTATGGGTACCCTAATGAAACATGGGAAGTTACCTTGCCTGCTGAGGAAGTTCCTCCGGAGATCCCTGAACCAGCTTTAGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g66420.2 (Oryza sativa), 3'ss of exon 2

-tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
  | | | |||| |     |   |     || |   ||  |  |||  |       || || | |  || | |   ||  | |   |   | | |    ||| |||||||| ||||| || ||||| | ||| |||||||||||||| ||||  ||||| | |||||||||||| || ||  | ||||| |||||||| ||
tgggcatacatagtagtagagcaacttctaagctctgaacactattactcagcagattgttcgtagggtttatgggtactaattcttctgttttga-acagAAAAGGAGAACTTGTGCCTTTATGGATATCCTAATGAAACATGGGAGGTGACCTTGCCAGCTGAGGAAGTGCCCCCAGAGATCCCTGAACCAGCATTGGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G008259_T02 (Zea mays), 3'ss of exon 2

-----------tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
            |||||  ||  |||   || |||  || |   |||| |     ||    ||  |  |  |  ||| |       |||  || ||   || |  ||| |||||| |||||| ||||| | |||||  |||| |||||||||||||||||||| |||||||  ||||| || |||||||||||||| ||||||||  | ||
cgaactttcctggtcctggat--tcttttaattagatagcatggaagaaaggatcttgacaaaaag--acctagaatct-------taaggttttgacgttttgtttgcagAGAAAGAGAATCTGTGTTTGTATGGTCTTCCCAATGAAACATGGGAAGTGAACTTGCCTGCAGAGGAGGTTCCTCCTGAACTTCCAGAGCCAGCTCTGGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1

tgtccttcataatctcccaaataggaagaacc-caagagaatgattttttgaagtgttatttgcaatgtgttttatt---aacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
    |||  |    |  ||| ||     | ||     ||| | |     ||||     |   ||||  |   |||||   || ||||| || || |  ||   | ||||||||| ||||| ||| |||||||  |||| ||||| ||||||||||| || ||||||| |||||| || ||||||||||| || ||||||||  | ||
---tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaac---aaccgcaa-ataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G153087_T01 (Zea mays), 3'ss of exon 2

tgtccttcataatctcccaaataggaagaacc-caagagaatgattttttgaagtgttatttgcaatgtgttttatt---aacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
    ||| ||    |      |     || |      ||  | |   | ||||     |  |||||  |   |||||    | ||||| || || |  ||     |||||||||||| || ||| |||||||  |||| ||||| ||||||||| | || ||||||| ||| || || ||||||||||| || ||||||||  | ||
---tcttgattcatttttgtttgaagtgagctattttaggtttagagtctgaaac---aactgcaa-ataccttattcgagatattattttcttttgttttgcacagAGAAGGAGAACTTATGTTTATATGGACTTCCTAATGAGACATGGGAAATAAACTTGCCTGCTGAAGAGGTCCCTCCTGAACTGCCAGAGCCAGCTCTTGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G02470.1 (Arabidopsis thaliana), 3'ss of exon 2

-------------------------------------------------------------------------tgtccttcataatctcccaaatag--gaagaacccaagagaatgattttttgaagt-gttatttgcaatgtg--ttttattaacattatgttattctcgtt---gtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
                                                                         ||   ||  | | ||   |  | |  |||        |  || ||||   | |  | ||  |   |  ||||  |||| || |   | | | ||||| |||   ||||||||||||||||||||||| |||||  |||||||||| |||||||| || ||| | || ||||||||||| |||||||| |||||||| ||||| |||||
gtgagttatttcttcacaacttttaaaaaattagtcttgcttagcttctatagtttctagtgaaatgttttgttgaagttgttgagcttgtatgttgttgaattgtgttggttaaagattgagttagttagtcctcctctgtgtggtttttctttaaggtgtttcattcttgtttatgtagAGAAGGAGAATTTGTGTCTCTATGGACTTCCAAATGAGACATGGGAGGTTAATCTACCCGTTGAGGAAGTTCCTCCTGAGCTTCCTGAACCAGCTTTAGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2

tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgt-tatttgcaatgtgttttattaacat-tatgtta--ttctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
  |  || ||| || |     |    |  | |||     ||  | | |||   |   |   |||||  || ||  ||   || | ||| |  || |  || ||||||||||||| |||||||| |||||  |||||||||| ||||||||||| ||  ||||||||||||| || |||||||| ||||| || |||||||||||
-ttattttatattcactt---tttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG

upper sequence: GLYMA07G40170.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S371_53V6.2 (Physcomitrella patens), 3'ss of exon 2

--tgtccttcataatctcccaaataggaagaacccaagagaatgattttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG
  | || |     |  |   |  |||   |  || | | |    ||   ||   |  || ||      || ||  || |   |||| || | |   ||| ||||||||||||||||||  ||||||| |||||| | ||| |||||||||| ||| | || | ||| || || |||||||||||||| || || ||  | ||
gttttcgtagggcaattttgaggtagttggtgcc-atgtgttacatcacttagcgctttgttatgtgagttttaaatgatttttatttt-tccaaattgcagAGAAGGAGAATTTGTGCTTATATGGTTTTCCAGAAGAAGCATGGGAAGTAAATCTACCAGCTGAAGAGGTTCCTCCTGAACTTCCAGAACCTGCTCTTGG

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|298198567|gb|HO040106.1|HO040106

EST:     ACGTTGAAAAGCTTTACCAGCAGTGCGATCCCG                         AGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGA
genomic: ACGTTGAAAAGTTTTACCAGCAGTGCGATCCCGgtgggttttc ... ctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGA

EST: gi|209720056|gb|BW659455.1|BW659455

EST:     ACGTTGAAAAGTTTTACCAGCAGTGCGATCCCG                         AGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGA
genomic: ACGTTGAAAAGTTTTACCAGCAGTGCGATCCCGgtgggttttc ... ctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGA

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttgaagtgttatttgcaatgtgttttattaacattatgttattctcgttgtagAGAAGGAGAATTTGTGTCTATATGGGTTTCCAAATGAAACATGGGAAGTGAATTTGCCTGTTGAGGAAGTGCCTCCTGAACTTCCTGAGCCAGCATTAGG

                           tattaac  putative branch site (score: 1)
                                        ttattctc  putative PPT
                  aatgtgttttattaac  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