ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

Basic information

species	Arabidopsis thaliana
transcript	AT1G55520.1
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgta-taaagtctagtaataaaattgctgattacattttgc-agGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                             ||   ||||  | ||   |  |   ||| | |||   | |  |      | | |||  ||| |     |||    |  ||   || ||| || | | | ||||||| ||||| ||||||||||| ||||| |||||||| ||||| || || ||||| || || |||||||| |||||| ||||||||||||||
--------------------------------------------gtaactatttcaagcttgcttgatt-ttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaa---ctcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                           | | |   ||  ||   | ||| ||||| ||||     ||       ||  ||   || ||     | || |||     ||||   |  |||   | ||||  | || |     ||||| || ||||| ||||||||||| || || |||||||| ||||| || || ||||| || || |||||||| |||||| ||||||||||||||
-------------------------gtaactatttcaggct---tgattaattttcatctgtgcaaa-------tgcctaccattttcattctgtaagattgtacctaaatgtt--taactcatttgc--actatac----cagGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtattt-ttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                           || || |   | || ||||  || |||||| |    |||  || ||           || | ||||    ||  | |   | | |      ||||  |||||||||| ||||| ||||||||||| || ||||||||||||||||| || ||| | || || || ||||| || |||||| | || ||||| |||
-------------------------------------------gtaatgccactctagctca--catcaattcattcagattgattgtcc----------ttgcttatatcagct--tgacgcattgga-----acatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                                           | | |     || | ||||||  || | | |       ||  |  | || |    |||    || |||||| |   |     |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||||||||| || |||||||| |||||| |||| |||||||||
----------------------------------------------------------gtaactttttcatacttgtgtacattgacctgttctttgaacaatatgtaca--tcagttgctaagttgctgttctaagc---cagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                                   |   ||| |  ||     | ||||||  |  | |       | | || ||    ||       ||| |  || |||||| |    | |  ||||| |||||||| ||||| ||||| ||||| |||||||| || || || ||||||||||| || ||||| || |||||| |||| |||||||||
--------------------------------------------------gtagctattttcat-----actcgtgtacagatctgagctttgaacaatttgtacat------cagtcactaagttgctgttc---tatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                        |     ||  | | | |      | | || ||  | |  | | |   | |||| |     |    ||  | | || |  |    ||  | |||    |||  ||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||||||||||||||||||
---------------------------------------gtacaacatctactctgaaaatt-ttatcagttgttttccactcta--cagaagtagtttgtggtcattga-tttattccttt--ttctttattctgcttt--agGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                           |||   ||| |  |      | | || ||  | |  | | |   | |||| |     |    ||  | | || |  |    ||  | |||    |||  ||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||| ||||||||||||||
-------------------------------------------gttcaacatctccaaaaattttatcagttgttttccactcta--cagaagcagtttgtggtcattga-tttattccttt--ttctttattctgcttt--agGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgc---agGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                               || |  || | |     ||| ||||  | |   || || ||      | | |    || |   |||    | | |      |   |  ||| |||   ||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||| ||||||||||||||
----------------------------------------------tttaaggttcaacatctccaaaaattt-tatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6

---------------gtactcatatgtctctctctggtcctgatccagcacacact--gtgttattcatttttatctcaatcaa--caattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattac-attttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                | ||||||    |  ||    |  |     ||| |    |      | |||  ||||  | || | ||  || || |   ||  |||| ||   |  |  |  || || |    | || ||||    |   ||  ||  ||  |  ||||||| || || ||||||||||| ||||| ||||||||||| ||||||||  |||| || ||||||||||| || ||| ||||||||||||||
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgta-gtgtttgat-tactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcat-ttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattac-attttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                         ||  |  |  |  | | |||||||| |   ||  |||   ||| |  | | |   |   ||  |  | |    || ||||    |   ||  ||  ||  |  ||||||| || || ||||||||||| ||||| ||||||||||| ||||||||  |||| || ||||||||||| || ||| ||||||||||||||
-----------------------------------------gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatg-ttgtgcttga---ttactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                        |     || |  | | |    |||   || ||  | |  | | |   | |||| |    ||  |   |  | ||  |       ||     ||   |  |  ||||||||||||| ||||| ||||| ||||| |||||||| || ||||||||| | || || |||||||| || || ||| ||||||||||||| 
--------------------------------------ggtacaacatccgctctgaa---aattgtcagttgttttccactcta--cagaagtagt--ttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                    |  || || |     | ||||     ||| |   ||  |||   ||| |  | | |   |   |   || | |   ||| |       |||   ||||   |||  ||||||| || || |||| |||||| ||||| ||||||||||| |||||||| | ||| || ||||||||||| || ||| ||||||||||||||
------------------------------------aatctttgctggaactgttta-----atccatgtttgctgttcttttctcactgtaactatg-tagtgtttgattactaattggttccttgggtattatgcttt--agGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6

------gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
       | |   ||  |||||||||     ||||  ||| ||   | |||||| |  || |    |  |      || |    | || ||||                 ||||  | ||  |       ||  | |||      || ||||||||||||| |||||||| || ||||| |||||||| ||||||||||| ||||||||||| |||||||| |||||| |||| || || || 
gtatttattccattacatctctctctctctgtgatgtagc-caatttctgttatgctattcttctcc--ttgtttttttgccactgttcttatt---------------ttatattgactgctg------ttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5

---------------gtactcatatgtctctctctgg--tcctgatccagcacacactgtgttattcatttttatctca-atcaacaattcgtgtgtatttttatcgga----aggaaaaattacg-tataaagtctagtaataaaattgctga-----ttacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                 | | || | | | |   |||  |||  ||   ||  | | | ||  ||  |   | | | |   |  |  ||| | | |||  || |||  |    ||  |     ||| | |  |   |   || |||| ||         |  | |||||||||||||||| || ||||| ||||| || |||||||| ||||||||||| ||  | || |||||| | || ||| ||||  ||   || ||||||
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggccta-attttgaaatggaaactgaacacgtgtagatcatttg-gagtaggttcatcttatcctagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacatt--ttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                                                                      |  ||||   |||  || | |   ||||      ||| ||  | |   |  |  | ||||||||||||||| ||||||||||| ||||| ||||| || || ||||| || ||  | || || || || ||| ||||  ||   |||||||| 
-------------------------------------------------------------------------------------gtatgaagacgaaaacacat-tgtggtctgagctcaaacttagtaacgtccgtgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

upper sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5

gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgat-tacatt-ttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
                                                                                      |  |||| | |||  || | |   ||||      ||| ||  | |  | |||  | ||||||||||||||| ||||||||||| ||||| || || || || ||||| || ||  | || || || || ||| ||||  ||   |||||||| 
-------------------------------------------------------------------------------------gtatgaagaagaaaacacat-tgtggtctgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

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|19874591|gb|AU235422.1|AU235422

EST:     TATGCTCGGATTGNTCAAAAGCTTGGCTTTCCTGCAA-GNTCAAG                         GATTTTAAGATACAGAACATT
genomic: TATGCTCGGATTGTTCAAAAGCTTGGCTTTCCTGCAAAGTTCAAGgtactcatat ... cattttgcagGATTTTAAGATACAGAACATT

EST: gi|47831853|gb|CK121537.1|CK121537

EST:     TATGCTCGGATTGTTCAAAAGCTTGGCTTTCCTGCAAAGTTCAAG                         GATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATT
genomic: TATGCTCGGATTGTTCAAAAGCTTGGCTTTCCTGCAAAGTTCAAGgtactcatat ... cattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATT

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

                                    tgctgat  putative branch site (score: 3)
               tataaagtctagtaat  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