Sequence
atgc intronic sequence ATGC exonic sequence...gtaaaacgttcttgattcataccttcaataaataatatacttccttcatttcttttttgtatttataattattttatatttttgttggctgtgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04130.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 11
-gtaaaacgttcttgattcataccttcaataaataatatacttccttcatt-tcttttttgtatttataattat-tttatatttttgttggctgtgtttt-cagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
| | | | ||| |||||| | | |||| ||| || || | | | || | | ||| || | ||||| || | || |||| |||| |||||||||||||| |||||||| ||||| ||||||||| ||||||| || | |||| ||||| |||||||| ||||||||||| |||||||||
tttttagcatactt-attcat---ctgatcaaatggtatttttaattaactgtattggtaatttttttagtgggatttatcttaacatataatgctttttatagGATAAAGATATTAGCTTGAGTGGGGAGCATGTAAGAGAGGGAATGACCTGCATTATTGCAGTGAAGGTCCCTAATCCAGAGTTTGAAGGGCAAACAAAG
upper sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 11
-gtaaa-acgttcttgattcataccttcaataaataatatacttccttcatttcttttttgtatttataattatttta--tatttttgttggctg-tgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
||| | || | | ||| | | | || | | ||| | | || | | || || | | | || | ||| |||| || ||||||| ||| |||||||| ||||| ||||| ||| |||| || ||| | ||||| ||||| |||| ||| |||||||| ||||||||||||
cataagtgaatgttttgcttaagtctttga-----agtgcacctttgaatcctgtttatccaaccaatgaaaaacataattaactagatcagttgctctttgtagGATAAGGATATTACCTTGAGTGGGGAGCATGTAAGAGAAGGAATGACATGCATCATTTCAGTGAAGGTCCCTAGTCCAGAGTTTGAGGGTCAAACAAAG
upper sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA19G31030.1 (Glycine max), 3'ss of exon 11
gtaaaacgttcttgattcataccttcaataaataatatacttccttcatttcttttttgtatttataattattttatatttttgttggc--tgtgtttt---cagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
| | | | || | | | ||| | || || || | || | ||| |||| | || | || | |||| | |||||||| ||||||| ||||||| || ||||| |||||||| | || ||| | |||||||||||||| || ||||||||||||||||| |||||||||
----tataatagcaaatgtctccctttgtctaaaatgga-ttattttatgaatagttcacaaagtggattcttttcattgttaaatagcattctgttctttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
upper sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G28290.1 (Glycine max), 3'ss of exon 11
gtaaaacgttcttgattcataccttcaat--aaataatatacttccttcatttcttttttgtatttataattattttatatttttgttggctgtgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
| || | || | | |||| | |||| | || | || || ||| | | ||| || | ||| | || |||||||| ||||||| ||||||| || ||||| |||||||| | || ||| | |||||||||||||| || ||||||||||||||||| |||||||||
ttgtaaaatagcaaatgcctccctttgtttaaaatggattgttttatgagttcacaaagtggattcttttcattgttaaatagcattctgctct--ttgcagGAGAAGGATATTACTCTAAGTGGCGAGCATGTGAGAGAGGGTCTAACATGTGTTGTCTCAGTCAAGGTCCCAAATCCTGAGTTTGAAGGACAAACAAAG
upper sequence: AT5G04130.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv08s0007g05120.t01 (Vitis vinifera), 3'ss of exon 11
------gtaaaacgttcttgattcataccttcaataaataatatacttccttcatttcttttttgtatttataattattttatatttttgttggctgtgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
| | || | | | || || | | | | | | | | | | | ||| | | | | | | ||| | ||| | |||||||||| ||||||| |||||||| |||||||| ||||||||||| || ||| | ||||||| || ||||| ||||| || |||||||| || || |||
tattttattagacttgatgaactcgtagttaaatttgaataaaaaatgagtggaagcagta---gtaactttcagcagtaaaagtttgttttgttt---cattcagGAGAAGGATATTACTTTAAGTGGCGAACATGTAAGAGAGGGATTAACATGTGTTATCTCAGTAAAAGTTCCAAATCCAGAATTTGAAGGACAGACGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttcttttttgtatttataattattttatatttttgttggctgtgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
tgttttc CT-rich tract
tcttttttgtatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaacgttcttgattcataccttcaataaataatatacttccttcatttcttttttgtatttataattattttatatttttgttggctgtgttttcagGAGAAAGATATTAGCTTAAGTGGGGAACATGTTAGAGAGGGATTGACCTGTATCGTCTCAGTCAAGGTTCCTAATCCTGAGTTTGAAGGTCAAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
gtaaaac
- - - - - - - - tcatacc
- - - - - - - - - - - - -caataaa