Sequence
atgc intronic sequence ATGC exonic sequencegtactactgcatgtttcgcgtggtttaatagaaattggtatagtgtttcctaatttacctttgttccaacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71220.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 7
-------------------------------------gtactactgcatgtttcg-cgtggtttaatagaaattggtatagtgtttcctaattta----cctttgttcc------aacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
| | | || | | | | | | || | | | | | | || || |||| || || | |||| ||||||| ||||||| ||||| | |||||||| |||| ||| ||||||||||||||||| ||||| ||||| |||||||| || ||||| ||||||||||| ||
gtatttaaaatatttttctcttttcctttgataattggaaagattggaagctggatcctattgtagttggcttcgatgaactgctttctaagttttcccccctctttccgattgtaacagATCTAGGACATCAAACTGTACAGAGAATTGTCCGTGCTTCTGATCCTCTGCAGTCAATGCAGGAAATAAATCAAAATTTCCCTAGCGTAGTTTCTTCCTT
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------gtactactgcatgtttcgcgtgg-tttaatagaaattggtata-gtgtttcctaatttacctttgttccaacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
|| | | || | ||| || ||| | | || | || || ||| | | || | ||||||| ||||||| ||||| | |||||||| |||| || || |||||||||||||| ||||| ||||||||||||||||| ||||| |||||||||| ||
gtatttaaaatatttttctcttttcctatgataattggaaagattggaagctgaatcctattgcagttggcttcaatgaacagtgttctaagttttttccccctctttttgatggtaacagATCTAGGACATCAAACTGTACAGAGAATTGTCCGAGCTTCGGATCCTCTGCAGTCAATGCAGGAAATTAATCAAAACTTCCCTAGCATAGTTTCTTCCTT
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 6
---------------------------------------gtactactgcatgtttcgcgtggtttaatagaaattggtatagtgtttcctaatttac-ctttgttccaacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
| | | | || || ||||| ||| || | | ||| |||| || ||| | ||||||| |||| || ||||| | ||||||||||||| ||||||||||||||| ||||| ||||| || || |||||||| || |||| |||||||||| ||
gtattgctgtattggaatattttctttttgtgattattggaattgattgataatttattcagtttagtagggtttaatgaactgtgctgtaatatatattttaatataacagATCTAGGGCATCAAACTGTACAGAGAATAGTCCGTGCCTCTGATCCTCTACAGTCAATGCATGATATCAATCAAAATTTCCCTAACATAGTTTCTTCTTT
upper sequence: AT1G71220.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------------------------------------------gtactactgcatgtttcgcgtggtttaatagaaattggtatagtgtttcctaatttacctttgttccaacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
| | | || || | | ||| | |||| | | | || ||||| | || ||||||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| |||||||| || || ||||| || ||||||||||||||||| ||
gtatttatcatgactgttgatgaaaagtatatgatttggggtttaaatttttgtcactattggtcatgaaaattatctgatttggattaattatttaaaataactgaaat-ttgcctaa--tgatgactttttaacagATTTAGGACATCAAACTGCACAGAGGATAGTTCATGCCTCTGATCCTCTGCAGTCAATGCAAGAGATCAACCAAAATTTCCCTAGTGTAGTTTCTTCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcgtggtttaatagaaattggtatagtgtttcctaatttacctttgttccaacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
tcctaat putative branch site (score: 2)
tttacctttgttcc CT-rich tract
tttaatagaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactactgcatgtttcgcgtggtttaatagaaattggtatagtgtttcctaatttacctttgttccaacagATTTAGGACACCAAACAGCGCAGAGAATAGTCCATGCCTCTGATCCTCTGCAGTCTATGCAAGAAATTAATCAAAACTTTCCTAGTGTAGTTTCTTCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA