Sequence
atgc intronic sequence ATGC exonic sequencegttattcgaaaatctgatactttgtttttgctctttcttcttctcaaactcgcgtaacagaaactctgtaatatctgtctccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G03910.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 7
gttattcgaaaatctgatactttgtttttgctctttcttcttctcaaactcgcgtaac----agaaac--------tctgtaatatctgtctcc-------gcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
| | | | || || || | ||||| | | ||| | ||| ||||| | | |||| || |||| |||||| |||| |||||||| ||| |||||||||||||||||| ||||| |||||||||||||| || || ||||| |||||||| |||
-------------gttagcttgtattctttctttctcttccttttaaaaaaggaaaacaataagaaataagccttgtttttaattactacctccttgctttgcagATTCTGAAAAAGAAAGGGGTTGTGATCCTCCCAGATATATTTGCAAATTCAGGAGGAGTCACAGTTAGCTACTTTGAGTGGGTGCAG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 8
gttattcgaaaatctgatactttgtttttgctctttcttcttctcaaactcgcgtaacagaaactctgtaa--tatctgtct---ccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
| | ||||| || || || | | ||| | || | | ||| | || || || |||||| |||||||||||||| ||| ||||||||||||| |||| ||||| |||||||| || || || || ||||| ||||||||||||
-------gttagtctgaattttctcttcctttcccttcttcaaacaagaaagaagaaatgcactattgttaactaccttcctaacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 7
gttattcgaaaatct-gatactttgtttttgctctttcttcttctcaaactcgcgtaacagaa-actctgtaatatctgtct---ccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
| | | | ||| | | ||| | |||||| | | | || | | | | | || || || |||||| ||||||||||||| ||| | ||||||||||| |||| |||||||||||||| || || || || ||||| |||||||| |||
-------gttagtttagattttctctttccttcccttcttcaaacaagaaagaagaaatgcactattgttaactaccttcctaacttgcagATTCTGAAGAAGAAAGGGGTTGTTATCCTCCCAGACATATTTGCAAACTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTCCAG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 8
----------------------------------------------------gttattcgaaaatctgatactttgtttttgctctttcttcttctcaaac-tcgcgtaacagaaactctgtaatatctgtctccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
| ||||| | | || | | |||| || | | | | | || || || |||||| |||| |||||||| ||| |||||||||||||||||| || || || ||||||||||| || || ||||| |||||||| |||
gttagtttgaattcttttttctgttccttttaataaaaaagcaacaaaaaaaaaaacaagaaaaagaaaaagaaaacattggaagaaaagtaagaacaaatatcatgca-ctgtttttaactacctccttactttgcagATTCTGAAAAAGAAAGGGGTTGTGATCCTCCCAGATATATTTGCTAATTCTGGAGGAGTCACAGTCAGCTACTTTGAGTGGGTGCAG
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G16320.1 (Glycine max), 3'ss of exon 9
gttattcgaaaatctg-atactttgtttttgctctttcttcttctcaaactcgcgtaacagaa-actctgtaatatctgtct---ccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
| | | | || | | ||| | |||||| | | | | || | | | | || || || | |||| ||||||||||||| ||| | ||||||||||| |||| |||||||||||||| || || || || ||||| ||||||
-------gttagtttacattttctctttccttcccttcttcaaacaagaaacaagaaatgcactattgttagctaccttcctaacttgtagATTCTGAAGAAGAAAGGGGTTGTCATCCTCCCAGACATATTTGCAAACTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGG------
upper sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 9
gttattcgaaaatctgatactttgtttttgctctttcttcttctcaaactcgcgtaacagaaactctgtaatatctgtctccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
|||| | ||| | ||| | || | | ||| ||| | || | |||| ||| | ||||||| | |||||||||||| | || || ||||| ||||| |||||||| || ||||||||||| ||||| || ||||||||||||
gttagtgcaaactttgaaatttaga----gttctgaaaaaaaaaaaaaaaactgcaatgccataactgttgtattctctt--gcagATCCTATCAAAGAAAGGTGTTGTCATTCTTCCAGACATATATGCAAACTCGGGGGGAGTCACTGTCAGTTATTTTGAGTGGGTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttcttcttctcaaactcgcgtaacagaaactctgtaatatctgtctccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
gcgtaac putative branch site (score: 3)
tctgtctcc putative PPT
tgtaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattcgaaaatctgatactttgtttttgctctttcttcttctcaaactcgcgtaacagaaactctgtaatatctgtctccgcagATCTTGAAGAAGAAAGGTGTTATGATCCTCCCAGATATATACGCAAACTCAGGAGGAGTCACTGTAAGTTACTTCGAGTGGGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG