Sequence
atgc intronic sequence ATGC exonic sequencegttagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G73670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 2
--gttagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctg---tttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
||| ||| | | ||| | || | || || ||| |||| || ||| | |||| | | |||||||| | ||| || ||||||||| | || || ||||| ||||| || ||||||||||||||| ||||| |||| || || || || || || || || |||||
gtagtagattccatatagtaggaa--atcggtaatttcttttgcttatgtggtt---gacacgctcactttctggtttctctttgcagCAAGTGTTTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGATTGCAAGCTGAAGGTTTGCGATTTCGGCCTTGCCCGAGTGTCATTTAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 2
---gttagtttc-----taaacagtctctttcact-tgtgttatcattatgatataaggttattgaagagctacgtctctgtttg--tttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
||||| || | | | || || | | ||||| | ||| | | || | ||| | | | ||| |||||||| | || || ||||||||| | || || ||||| ||||| || |||||||| |||||| ||||||||||||| ||||| || || || || || || ||
gttgttagactccacattgagtggacttgttaatggtttgtta-cgttacttcttgtgagc-ttcagtttctatgcttgttcttggttttgcagCAAGCGTCTTCCATCGGGATCTTAAGCCCAAGAATATTCTAGCCAATGCTGACTGCAAGCTGAAGATTTGTGATTTTGGCCTTGCCCGCGTTTCATTCAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 2
gt-tagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
|| | || || | | | | | || | || | | ||| | |||| || || || | || ||||||| |||||||||||||| |||||||| ||||| |||||||||||||| ||||||||||| | || || ||||| ||||| || ||||| || || |||||
gtattgtatccttattatgacaaggtccttccttgacttttttagatagtgatattaaactagtatatcatttttc--ttgcagCAAATGTGTTTCATCGTGATTTGAAGCCAAAAAACATTCTTGCTAACGCTGATTGCAAACTAAAAATATGTGATTTTGGGCTTGCTCGAGTTTCATTTAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 2
gttagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
|| || ||| | || || ||| || | || ||||| | || | || | | || ||||||| |||||||||||||| || ||||| ||||| || ||||| |||||||||||||||||| | || | ||||| ||||| || ||||| || || |||||
gtatccttgtaattaag-tccttgactgttgctg--atagtgataataaacta-----aaataacattt----tttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTGATTGCAAGCTAAAATTATGTGATTTTGGACTTGCTCGAGTTTCATTTAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 2
gttagtttctaaacagtctctttcacttg--tgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
| | | | | | || | || | || | | ||| | |||| || | || | || ||||||| || ||||||||||| |||||||| ||||| || ||||||||||| ||||||||||| | || || ||||| ||||| || ||||| || || |||||
-----gtattgcatccttattataaccaggtccttgacttttttagatagagatattaaactagtgtatcatttttc--ttgcagCAAACGTGTTTCATCGTGATTTGAAGCCAAAAAATATTCTTGCTAACGCTGATTGCAAACTAAAAATATGTGATTTTGGGCTTGCTCGAGTTTCATTTAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 2
gttagtttctaaacagtctcttt-cacttgtgttatc-attatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
|| || || | || || | | | | | | || || | | | | | | | ||||||| |||||||||||||| || ||||| ||||| || ||||| ||||||||| ||||||| | || || ||||| || || || ||||| || || |||||
---------------gtatccttgtaattaagtccttgactgttgcagatagtgatattaaactaaaataacattcttcttgcagCAAATGTGTTTCATCGTGACTTGAAGCCAAAAAATATTCTAGCTAATGCTAATTGCAAACTAAAAATATGTGATTTCGGACTTGCTCGAGTTTCATTTAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0011g04920.t01 (Vitis vinifera), 3'ss of exon 2
-------gttagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
|| |||| ||| || | || | | | || | | | |||| | | ||| | | | || |||||||| |||||||||||| | ||||| || ||||| ||||| ||||||||||| || ||||| ||||||||||||| ||||| || ||||| || || |||||
gttggacctttgttta-aaattgtgccattatcgtat-ttcttttggttctatattctcaatgaccaataatattgtctttattttgcagCAAATGTGTTTCATAGAGATTTAAAGCCAAAAAACATCCTTGCTAATGCAGACTGCAAACTGAAGATTTGTGATTTTGGGCTTGCTCGCGTGTCATTTAA
upper sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 2
---gttagtttctaaacagtctct---ttcac--ttgtgttatcattatgatataa--ggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
| | ||| | | | | | |||| || || ||||| | | || | | | | | | | || || || |||| |||||||||||||| |||||||| ||||| || |||||||||||||| || |||||||||||||||||||| ||||| || ||||| || || || ||
gttggtgcttttcagagatattatagcctcaccgtttgtttgcttttatgtcctgaatggccactaataaa--aattttatggtttcttccagCAAATGTGTTTCATCGAGATTTGAAGCCAAAAAATATTCTTGCTAATGCCGACTGCAAGTTGAAGATTTGTGATTTTGGGCTTGCTCGGGTGTCATTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
tctctgttt CT-rich tract
atcattatgatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtttctaaacagtctctttcacttgtgttatcattatgatataaggttattgaagagctacgtctctgtttgtttgcagCGAATGTGTTTCATCGGGATTTGAAACCAAAGAACATTCTTGCTAATGCTGATTGCAAGTTGAAGATTTGTGACTTTGGTCTAGCTCGTGTATCTTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA