Sequence
atgc intronic sequence ATGC exonic sequencegtaccaaacgctctttattctttatggtagaaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatattagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G67850.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
-------------------------------gtaccaaacgctctttat--tctttatggtagaaaatagtttggtgtgtttatgactac-------tgactcccttggcacctggaaatata-----ttagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
||| || || | | ||| | | | | |||| ||| | | | | | | | | | ||| || | | | | ||||||||||||| ||| ||||| |||| ||||| ||||| ||| |||||| ||||| ||| | |||||||||||||||||||| ||||||||||| ||||||
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagt-gtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
-------------------------------gtaccaaacgctctttattctttatggtagaaa-atagtttggtgtgtttatgactac-------tgactcccttggcacctggaaatata-----ttagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
|| ||| || || | ||| || || | | ||| || | | | | | | | | ||| || | | | ||||||||||||| ||| ||||| |||| ||||| ||||| ||| |||||| ||||| ||| | |||||||||||||||||||| ||||||||||| || |||
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------gtacca--aacgctctttattct-ttatggtagaaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatat-----tagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
||||| | | ||| || | ||| | | || | | || || | | | ||| | || | |||||||||||| ||| ||||| |||| ||||| ||||| ||| |||||| ||||| || | |||||||||||||||||||| || |||||||| ||||||
gtaagaatccattgcgctcgatcgtaaatattggatgacaaattttccttgcaacttttaccattattattgtttgcctaactaaaatcaaaagtgttctgct-tattcatctatgttatgatattaagcatttaattattttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAA
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------gtacca--aacgctctttattct-ttatggtagaaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatat-----tagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
||||| | | ||| || || ||| | | || | | || | | | | ||| | | | |||||||||||| ||| ||||| |||| ||||| ||||| ||| |||||| ||||| || | |||||||||||||||||||| || |||||||| |||||
gtaagaatccattgcgctcgatcataaatattggatgacatattttccttgcaactcttaccatcattattgtttgcctaactaaagtcaaaagtgttctgctaattcaatca-tgttatgatattaagcatttaatttttttccctcctagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATTTTTATATGGGATGAAGACCTGGGTGTTGAACATTTTAATGCAGAG
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 5
gtaccaaa---cgct-ctttattctttatggtagaaaat--agtttggtgtgtttat-gactactgactcccttggcacctggaaata-tattagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
||| ||| | || ||| | | | || || | | |||| ||||| | | | ||| | | | | | ||||||||||| ||||||||| | || || || ||||| ||| |||||| ||||| ||| | ||||||||||||||||| || ||| |||| || ||||||
gtaaaaaagttctctgcttaaattctcattgtgtcatttccagttaatattgtttgccaaacttaaaatggtttgttatttctttttcctctcagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGCACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCAGAA
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 5
gtaccaaac--gctctttattctttatggtagaaaat----agtttggtgtgtttat-gactactgactcccttggcacctggaa-atatattagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
||| || ||| | | || || || | | || |||| |||||| | | | ||| | | | ||||||||||||| ||||||||| | || || || ||||| | | |||||| ||||| ||| | ||||||||||||||||| || ||| |||| || || |||
gtaaaaattctatgcttaaattttcattgtggcatattttcagttaatattgtttaccaaacttaaaatggtttgttatttctttcgcctcttagGTGGTATGCCAAGAGGTTTCTACATCCAGACATTGTGGTACCATATGACTATATTTTCATGTGGGATGAAGACCTGGGGGTTGAGAATTTCAATGCTGAA
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
------------------------gtaccaaacgct--ctttattctttatggtag-----aaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatat--tagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
| ||| || | | ||| |||||| || | | |||| ||||| || | ||| | || || || | | | |||||||||||| || || ||| |||| ||||| ||||| || |||||| ||||| || ||||||||||||| || || || ||||||||||| ||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattc---tttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
------------------------gtaccaaacgct--ctttattctttatggtag-----aaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatat--tagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
| ||| || | | ||| |||||| || | | |||| ||||| || | ||| | || || || | | | |||||||||||| || |||||| |||| ||||| ||||| || |||||| ||||| || ||||||||||||| || || || ||||||||||| ||||||
gtaaggagcttctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattc---tttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatagtttggtgtgtttatgactactgactcccttggcacctggaaatatattagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
tactgac putative branch site (score: 1)
aaatatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaccaaacgctctttattctttatggtagaaaatagtttggtgtgtttatgactactgactcccttggcacctggaaatatattagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA