Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtttatcagctatagctcttagtggtttagttttcctagtccatgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57870.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
gtaaagtttatcagctata-gctct--tagtggttt--agttttcctagtccatgcttagattatg---acgtg-tcatggtccac-agGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
|||| | | | | ||| ||||| |||| | | || | | | | || | || | ||| | | | || |||||||||||||||| ||| |||||||||| |||||||||||||| ||||| || || || || ||||| |||||||| || |||||||| ||||| ||||
gtaagatat-tgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
-----gtaaag-tttatcagctatagctcttagtgg--tttagttttcctagtcc--atgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
|| | | || ||| | ||| ||| || | || | |||| | | || ||| | || || ||||||||||||||||| ||| |||||||||| |||||||||||||| ||||| || || || || ||||| ||||| || || |||||||| ||||| ||||
gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatg-tgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 6
gtaaagttta--tcagctatagctcttagtggttt-----agttttcctagtccatgcttagattatgac--gtgtcatggtcca-cagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
||||| ||| |||| | | | ||| |||| | ||| || | | ||| | ||| || | | | | | ||||| ||||||||||||||| ||||||| || || |||||||| || ||||||||||| ||||| ||||| ||||| || || || ||||| ||||| || |
gtaaattttcatccagcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagctttccgttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCCCCAGAACTCATATTTGGTGCCACTGAATATACGACTGCTATAGATATTT
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtaaagtttat--cagctat----agctcttagtggtttagttttcctagtccatgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
| | | || | | | ||| | ||| ||| || | || | | |||| | || | ||||||||||| || |||||||| || ||||||||||| | ||||| ||||| || ||||| ||||||||||| || |||||||| ||||| ||||| ||||
ctgacgagttgttcgagaagacttcgtttctggtatgcggatgtctcagtaagcgggtgcgtgtgaatagtgatgtaaccgagacgggct-tgttgtgcagGTGAAAGGGGAGCCCAATATCTCGTACATTTGTTCGCGGTACTACCGTGCTCCGGAGCTTATTTTTGGAGCGACGGAGTACACGACTGCCATAGATATAT
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------gtaaagtttatcagctatagctcttagtggtttagtt---ttcctagtccatgcttagattatgacgtgtcatgg--tccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
| | | | | | | | || || |||| | | | | || | ||| || | | || | ||||||||||| || || |||||||| |||||||||||| |||| || ||||| || ||||| || |||||||| || || ||||||||||| || |||||||
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggta-ttcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------------------------gtaaagtttatcagctatagctcttagtggtttagtt-ttcctagtccatgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
|| || | | | | || || || | | | || | || | || | | | || || | ||||||||||| || ||||||||||| |||||||||||| | ||||| ||||| || ||||| ||||||||||| || |||||||| ||||| || || ||||
gtgagtatctgttggatgagagtgagcattgttcaaattgtgaggctgtgaaccatccagtggaatggactttacttgtgtggtggagatgttgcactaattcctgattagggtacttctcggtggagcg-acatgacggag-gtggtgttgtgcagGTGAAAGGGGAGCCCAATATTTCGTACATTTGTTCACGGTACTACCGTGCTCCTGAGCTGATTTTTGGAGCGACAGAGTACACGACTGCCATCGATATAT
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------------------------------------gtaaagtttatcagctatagctcttagtggtttagtt--ttcctagtcca-tgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
|| || || | | | || | || | | ||| || | | || | | || ||| | ||||||||||| || ||||| || || |||||||||||| | ||||| ||||| || ||||| ||||||||||| || |||||||| ||||| || || ||||
gtgagtatctgttggatgagagtgagcgttgttcgagttgtgaggctgtgaaccacccagtggaatggactgtacttgtgtggtgtagatgttgcactaattcccgattagggtacttctcggtggagcgacatgacggaggtg-gtgatgttgtgcagGTGAAAGGGGAGCCCAACATCTCGTACATTTGTTCACGGTACTACCGTGCTCCTGAGCTGATTTTTGGAGCGACAGAGTACACGACTGCCATCGATATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtggtttagttttcctagtccatgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
tttagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtttatcagctatagctcttagtggtttagttttcctagtccatgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG