Sequence
atgc intronic sequence ATGC exonic sequence...ataagtattcactgccaacaatcttaactatctgactggtccgtgggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01130.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g02884.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------ataagtattcactgccaacaatct-----taactatctgactggtccgtgggcttacat-ttagtgatatttattgt-tgattctca-----tgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
|| | ||| ||| | |||| | ||| ||| | | | | | ||| | | | | ||| | | ||| | | ||| | | | ||||| |||||||||| ||||| || | ||| || ||||||||||||| || ||| | ||||| ||||| || ||||| || ||||||||||| ||| |
gtgtttttctcttgttggagtattactaattttatttttttcgtaacactttgaatgaatttgcattttctggaatcaatatgctaataaatatttttttttaactttaacacgcatatcatcaacttctatcatatcattttggctaattaaattgtataacaatttagAGACGAGGAAGAGCTGGTCGAGTCCAACCAGGGGAGTGTTACCATCTATATCCACAATGCGTGTATGAAGCATTTGCTGACTATCAGTTGCCAGAACTCC
upper sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G25800.1 (Glycine max), 3'ss of exon 14
ataagtattcactgccaacaatc-ttaactatctgactggtccgtgggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
| ||| || ||| |||| || | ||| | | | | ||||||| | ||| | | || ||| || |||||||||||||||| ||||| |||| ||| ||| ||||||||||||| || || | || || ||||||||||||||||| ||||||||||| |||||||
accagtgaattttgaacttaattattaatcatgaatgaaattattggacct-taaatgctgatattgttatctgaattttcccctgatcctgtttttctagAGAAGAGGAAGAGCTGGTCGGGTTCAACCAGGAGAGTGTTACCATCTCTATCCTAGATGTGTGTATGATGCTTTTGCAGAGTATCAGTTGCCAGAAATTT
upper sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G18490.1 (Glycine max), 3'ss of exon 6
ataagtattcactgccaacaatctta-actatctgactggtccgtgggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
|| || | | ||| || | || || | || ||| | | | | ||| | || || | ||| | | |||||||||||||||| |||||||||| ||| ||| | ||||| ||||| || || | || ||||||||| |||||||||| |||| || ||||||||||
gcaattacctgtgaaccatgatcctacattaactaaa-accatttgaccttttaacgactttattctatcctcccactaaattctttttttttttctctagAGAAGAGGAAGAGCTGGTCGTGTTCAACCAGGAGAATGTTATCATCTCTATCCTAGATGTGTATATGATTCTTTTGCAGAGCATCAATTACCTGAAATTT
upper sequence: AT2G01130.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv01s0011g04360.t01 (Vitis vinifera), 3'ss of exon 11
ataagtattcactgccaacaatcttaactatctgactggt--ccgtgggcttacatttagtgat--atttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
|||| | | || | || ||| | | | | ||| ||| || | || |||| | ||| ||||| ||| | || | |||||||||||||||| || ||||||| ||| ||| | ||||||||||| || || || |||||||||||||||||||| ||||| |||||||||||||
---ctgattccttccaaattacattgacttagaaaataggaatcaagggtttattgcatatgtttgatatattttcctttcctatgctttgtctaatat-gtagAGAAGAGGAAGAGCTGGCCGTGTTCAACCAGGAAAATGTTACCATCTCTATCCTCGATGTGTATATGATGCTTTTGCAGATTATCAATTGCCTGAAATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
atttagtgatatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataagtattcactgccaacaatcttaactatctgactggtccgtgggcttacatttagtgatatttattgttgattctcatgctctgtttgtgattgcagAGAAGAGGAAGAGCCGGTCGTGTTCGACCTGGACAGTGTTACCATCTTTACCCAAAGTGCGTATATGATGCTTTTGCAGAATATCAGTTGCCTGAAATTT
- - - - - - - ccaacaa
- - - - - - - - - - - - - -ctatctg
- - - - - - - - - - - - - - - - - -ctggtcc
- - - - - - - - - - - - - - - - - - - - - - - -cttacat