Sequence
atgc intronic sequence ATGC exonic sequence...cgttttcttatactctttgcttatcaatgtgacatcgtcctttggctcactttattccaaggcatgtccactcatagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G47020.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA11G04290.1 (Glycine max), 3'ss of exon 15
cgttttcttatactctttgcttatcaatgtgacatcgtcctttggctcactttattccaaggcatgtccactca---tagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
|||| || || | | | || | | | || | | | | ||| ||| | | ||| | | | | ||| ||||||| || ||||||||||| || |||||| ||||||| ||||| || ||||||||||||||||| || || |||||||| || ||||||||| |||||
--aaagcttaagctgttaggtgaa-aacacatgactggctttatattacttctctaacaataattgtgattttaagttagatttaatcctaactgtgatgcagGTATGAGGATGCTTTTAATAGATTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCAGTTGTTGCA
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA01G41140.1 (Glycine max), 3'ss of exon 15
cgttttcttatactctttgcttatcaatgtgacatcgtcctttggctcactt-tattccaaggcatgtccactca---tagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
| | | | ||| | | |||| | | || || |||| | | ||| ||| | | ||| | || ||| ||| ||||||| || ||||||||||| || |||||| ||||||| ||||| || ||||||||||||||||| || || |||||||| || ||||| ||| |||||
tactattccaaaaccttaagctgttgg-gtgaaaacaca---tgactgacttctctaacaataattgtgattttaagttagatttgatcataactgtgatgcagGTATGAGGATGCTTTTAATAGGTTTATTGATGAAATCAACTCGGTTGCTGCATATGATTGGTGGGAGGGATCAGTGCACAGTATACTTTCTGTTGTTGCA
upper sequence: AT5G47020.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv02s0012g00460.t01 (Vitis vinifera), 3'ss of exon 15
-cgttttcttatactctttgcttatcaatgtgacatcgtcctttggc-tcactttattccaaggcatgtccactcatagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
| ||| | || | | || | |||| | || | || | | |||| || |||| || ||| ||||| |||| |||| |||||| ||||||||||||||||| || ||| |||| || || || || ||||||||||||||||||||||| || |||||||| |||||||| ||||||
ttagaagcctattgtattggaagaacatattagcatcaggttgtgccatctcatgattcaaaaaaatgttttctaata-ttctgactattt-tgatctacagGTATGAAGATGCTTTTAACAGATTCATTGATGAGATTAATTCAGTTGCTGCATATGATTGGTGGGAAGGGTCAGTACACAGCATACTTTCAGTGCTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcactttattccaaggcatgtccactcatagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
ttctgat putative branch site (score: 3)
catttct CT-rich tract
tttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgttttcttatactctttgcttatcaatgtgacatcgtcctttggctcactttattccaaggcatgtccactcatagttctggacatttctgattcgcagGTACGAAGATGCTTTTAACAGCTTTATTAATGAAATAAACTCTACCGCAGCATATGATTGGTGGGAAGGGTCTGTGCACAGCATTCTTTCAGTTCTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - ctctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcata