Sequence
atgc intronic sequence ATGC exonic sequence...ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G36850.1 |
intron # | 38 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: GRMZM2G326643_T01 (Zea mays), 3'ss of exon 37
----------------------------------ttcagcactcgttttccggtttattggattgt-ttttatttaatctattaccactt-tccagtgacagcttagtttcaa--------tttgttcaaaactaatcttg--cagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
| || | | ||| | | | | || | | | | | | ||||| | | | | | |||| | | || | |||| |||| ||||||||||||||||||||| ||||| ||||| || ||| | |||||||| ||||| || || || || ||||| || || || || ||||| || || |||
gtgagtaaattttaccaaccatatggtagcatgctatagggaacatgttctgttgcactctcttatactgcagtcattttattatgatatatttgacaataatttagaactgagctaacttctggtggtatactatccttgttcagAGTTCGAATGCACTATGGACATCCTGATGTTTTTGATCGGATATTTCACATAACCCGAGGTGGCATTAGCAAGGCGTCTCGAGTGATTAATATAAGCGAA
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: GLYMA04G36710.1 (Glycine max), 3'ss of exon 15
------ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
|||| |||| | ||| | | | ||| | || |||| || | | ||| ||| | |||| ||||||||||||||| ||||||||||| || |||||||| || || ||||||||||| |||||||| ||||| || || || ||||| ||||||||||| || ||||||
aatatcttcattttcaattttatattctatcaaacaatgcatttttg--tagagattttgtttcagtt-catcctgtttttgattgggggaaaa---atcttgcagAGTTCGCATGCACTATGGACACCCAGATGTATTTGACAGAATATTTCACATAACTCGAGGAGGCATTAGTAAGGCATCACGTGTTATTAATATTAGTGAA
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: GLYMA06G18220.1 (Glycine max), 3'ss of exon 19
----ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA--
|||| | |||| | ||| | | | |||| | | || | || | | ||| || | |||| ||||||||||||||| ||||||||||| || |||||||| || || |||||||||| |||||||| ||||| || || || ||||| ||||||||||| || |||||
tatcttcatttttaattttatattctatcaaacaatgcattttta--tggagattttgtatcaatt-catcctgtttttggttggggaaaaa---atcttgcagagTTCGCATGCACTATGGACACCCAGATGTATTTGACCGAATATTTCACATAACTCGAGGAGGCATTAGTAAGGCATCACGTGTTATTAATATTAGTGAGGA
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: Vv17s0000g10010.t01 (Vitis vinifera), 3'ss of exon 32
---ttcagcactcgttttccggtttattggattg-tttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
||| ||| ||| ||| || ||| ||||| ||||| || | | ||| | || | | ||| ||| || ||||||||||||| |||||||| |||||||| ||||||||||| |||| ||||||||| |||| || || ||||| |||||||| ||||| ||||| || ||||||
attttcttttctctctttttttttttttcttttggtttttgtttaaaagat----gttctgcagataggactgatgaatcacatgtcttaaaacaaccttgcagAGTTCGTATGCACTACGGGCATCCTGATGTGTTCGACCGAATTTTTCATATATCTCGAGGTGGCATCAGTAAAGCATCACGTGTAATTAATATTAGTGAA
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: PP1S13_132V6.1 (Physcomitrella patens), 3'ss of exon 37
ttcagcactcgttttccggtttattggattgtttttatttaatct----attaccactttccagt-gacagcttagttt-caatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
| | | || | | |||||| |||| |||| | | | || || | ||| |||||| |||||| | | || |||||| ||||||||||||||||||||||||| || || | || || || || || | ||||| || ||||| ||||| || || | ||||||
cctatccacaaaatcggggaattccgatttgtttctatt--atctggaaaccaatagttccctttcgactatttagttagcaatttact----gtgtgttttacagAGTGAGAATGCACTATGGGCATCCAGATGTCTTTGACCGCATTTTCCACATCACAAGGGGAGGCATTAGCAAGTCATCCAAGCAGATCAATCTTAGTGAA
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: PP1S18_300V6.2 (Physcomitrella patens), 3'ss of exon 16
ttcagcactcgttttccggtttatt-ggattgtttttatttaatctattacc--actttccagtgacagcttagtttcaatttgt--tcaaaactaatctt--gcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
|| | || |||| ||| || || ||||| | |||| | | | | ||||| | | || | | || |||| || ||||||||||||| ||| |||||||||| ||| |||||||||| ||||| | ||||| | ||||||||||| || || |||||
-------gtcatggtcataattatcaggaccattatttgagaatctgcttatgaacttcatactagtaaatggtgcacaattcatgattaatatatgtgttatgcagGGTGAGAATGCACTATGGACATTCAGATGTGTTTGATCGAATATTTCACATAACGAGAGGAGGTGTAAGCAAAGCATCAAAGCAGATCAATCTCAGTACG
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
|| | ||| | || |||| | || || | ||| ||| || ||||||| || || ||||||||||| ||||||||||| || |||||||| | || || || || ||||| || || || || ||||| |||||
-------------------------------------------gtaagtctactcttggtagaacttgtagtgttaa------cagtttttatc---cagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
upper sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
lower sequence: EFJ05083 (Selaginella moellendorffii), 3'ss of exon 37
ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
||| || | | || || | || | | | || | | | ||||| || ||||||| || || ||||||||||| ||||||||||| || |||||||| | || || || || ||||| || || || || ||||| |||||
----------------------------------------------gtacgtctattct-tggtag---aacttgtagt--gttaacagtttttatgcagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
aactaat putative branch site (score: 2)
tttcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - -ggtttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaaac