ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC

Basic information

species	Arabidopsis thaliana
transcript	AT2G46770.1
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1

catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatt-tttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
    | || | |||   ||  || | | | |  |   || | |   | |   |  |  | || |    | |  | | ||  |||  |   |   |||||||||| ||| |  || ||  ||  ||| |||||||||||||| ||||| |||||||||||||| || || |||||||| ||||| || ||| | || || ||
---gtacgtaattaagcac-acacacatcga--tcaattcgatcgatttttgacatgtt-ttgatcaatgtggcatgtgtgtatcatacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1

------------------------------------------catattcggagttagttactgcaaagaccaacataggtttggttattatacaattta--ctatttaagt--ttttttcttctgattatttttgtcgttat-gcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                                          |  ||||  | ||  |  || | ||  | |  || | |||    || |  | |  ||  |||  |||||  |  | | |    |  || | | | ||  | ||||||| |||||| || ||  ||  ||| || ||||||||||| ||||| |||||||||||||| || || |||||||| ||||| || ||||| || || ||
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1

---------------------------------------------------------------------------------------catattcggagttagttactgcaaagaccaacataggtttggttattatacaatt-tactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                                                                                            |    || |  |    | |  |  ||| |  | | | | ||  |||     |     | |   |      |  | ||   || ||     |||||||||  || || || ||  |    || || ||||||||||| ||||| |||||||||||||| || || |||||||| ||| | || ||| | || || ||
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagct-gatcatcgtacgtccatggcgctgatcatcggggttagttatcgattctgcgtgcatgcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1

-------------------catattcggagttagttactgcaaa-----------gacca-acataggtttggttattatacaatt-tactatttaagtttttttcttctgattatttttgtcg----------ttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                   ||    ||   ||  || ||||| |           | |||  ||||  |     |    | |   |   ||     |    | |    | |||  |  | ||||            ||||||||| |||    || ||  |    || || ||||||||||| ||||| |||||||||||||| || || |||||||| ||| | || ||| | ||||| ||
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgtctatgcggccatgcatacatgcctctgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtgaccgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1

catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgtt---atgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
   ||     |  |   | | ||  |  |   |     | | | |  |       ||||| | |||    |  || |     ||   ||    |     |||||||  || || || ||  |    || || ||||||||||| ||||| |||||||||||||| || || |||||||| ||| | || ||| | ||||| ||
---atcaaacgcgatcgaattcatcgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1

catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                         ||  |   |   |||| | | ||   ||  ||  ||| | |  |  | | | | |||| ||   | ||   ||||||||||| ||||||||||  |  ||||||||||| ||||| || || |||||||||||||| || || || |||||||   | || ||| | ||||    
-----------------------gtgatgattttt--tttgctcagtagctaagata--attgatgagtagtgcatgtaattaattaatttgt---gcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G44910.1 (Glycine max), 3'ss of exon 1

catattcggagttagttactgcaaagaccaacataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                             |  ||   |||| | | ||   ||  ||  ||| | |  |  | | | | |||  ||   | ||   ||||||||||| ||||||||||  |  ||||||||||| ||||| || || ||||||||| |||| || || || |||||||   | || ||| | |||||   
--------------------------gtgatgatttttttgctaagtagctaagata--attaatgagtagtgcatgtaattgattaatttgt---gcagAGATGTGCAAAATAGGAAGCAGCCCACAAAACGATTGGTACTTGTTCAGCCACAAGTACAAGAAGTACCCCACGGGAAGCCGCACAAACCGCGCCACCAG

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1

--------------------------------------------------------------------------------------catattcggagttagttactgcaaagaccaa-cataggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAAT-AGGAACAAC--GCCA------CAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                                                                                        ||||  || | |  |  ||    |  | | |   ||  | |  |||| |     |      || ||            |       ||| || || ||||  |||| |  ||  || || ||   |||      |||||||||||||| ||||| |||||||| |||||||| || ||  |||| |   || | ||| |         
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccgatgtggtcat-cagAAGTGTGCAGGATTGGGGACGACCCACCAGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG---------

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1

-----------------------------------------------------catattcggagttag--ttactgcaaagacca---acataggtttggttat-tataca-atttac-tatttaagtttttttc---ttctgattatt---tttgtcgttatg-------cagAGATGTGTAAAATAGG-AACAACGCCAC--------AAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                                                      | |   |||  | |  ||| | | | ||  |   | |||| | ||| ||| |||| | || ||  ||| | ||  |  |     | ||||| |     | |||  ||  |       ||||| |||| | ||| ||  || ||||  |        | | ||||||||| ||||| |||||||||||||| |||||||| || ||||   |  | ||| |         
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGACGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG---------

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1

----------catattcggagttagttactgc-------aaagaccaacat----aggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
          |||      || |  | | | |       ||| |||    |    | || |     || || |  |  ||  |     |    ||     |||   |||| |   |  ||||   |||   ||| ||  |  ||   ||  |||| ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| || ||||||||||| | 
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccac-acacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1

------------------catattcggagttagttactgcaaagaccaacat----aggtttggttattatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC
                   |  |||  | || |  |    ||| |||    |    | || |     || || |  |  ||  |     |    ||     |||   |||| |   |  ||||   |||   ||| ||  |  ||   ||  |||| ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| || ||||||||||| | 
gtaagacggtcatccctcaagcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatgaattgcgtttgccac-acacagAACGGTGCCGAATTGGCTCCGCGGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

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|86053372|gb|DR349129.1|DR349129

EST:     TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAG                         AGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCC
genomic: TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttcc ... cgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCC

EST: gi|19875621|gb|AU236452.1|AU236452

EST:     TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAG                         AGATGTGTAAAATAGGAACAACGCCACA
genomic: TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttcc ... cgttatgcagAGATGTGTAAAATAGGAACAACGCCACA

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttatacaatttactatttaagtttttttcttctgattatttttgtcgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCCACAAGGACAAAAAATATCCGACGGGAACGAGAACTAACAGAGCCACTGC

                             ttctgat  putative branch site (score: 3)
                                      tttttgtc  putative PPT
      aatttactatttaagt  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