Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaagataatattctattgacaaattaattgatatatcgagtatggcaaatgatgtccatctttgattaattcaagGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65510.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G02760.1 (Glycine max), 3'ss of exon 4
-----------------gtaagcaagataatattctattgacaaattaattgatatatcgagtatggcaa-atgatgt--ccatctttgattaattcaagGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
|| | | | || | || | ||| | || | | | |||| ||| | | | | | | |||||||||||| |||||||| | || || ||||| ||||| ||||||||| |||| ||||||||| | |||||||| || || || ||
catttagatttacttcaagaaatctgctcaacttatcttaaaaaaatttatgttgtttgagagatggttttgtgacatagtaaattgtcgtggttatcagGTGGATATGATAAGGAAGAAAAGGCCGCGAGAGCTTATGATTTGGCAGCTCTAAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G33240.1 (Glycine max), 3'ss of exon 4
-------------gtaagcaagataat-attctattgacaaattaattgatatatc----gagtatggcaaatgatgtccatctttgattaattca--agGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
||| | | | | | |||| || | || | ||| ||| | | | | ||| | || | |||||||||||| |||||||| | || |||||| | ||||| ||||||||| | || ||||||||| | |||||||| || || || ||
atttatatttacttcaagaatgctcctcaacctatcctaaagcttttttctgtattttgagagatggttttgtaacatagtgaattgtcttgtttatcagGTGGATATGATAAGGAAGAAAAGGCCGCTAGATCTTATGATTTGGCAGCTCTGAAGTACTGGGGTCCCACTGCTACCACCAACTTCCCT
upper sequence: AT5G65510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s1291g00010.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtaagcaagataatattctattgacaaattaattgatat-atcgagtatggca--aatgatgtccatctttgattaatt-caagGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
| | ||| |||| | || | ||| | |||||| | ||| ||| ||| | |||| |||||| |||||||||||||| | ||||| || |||||||| || |||||| |||| ||||||||| || |||| ||||| ||||| ||
cgttcgcttcctttgttctttctaacaaatcctctaatactgggttgaacagtattacagagtattaaattaattatgatggacttgtgtaaattatcagGTGGGTATGACAAGGAAGAAAAGGCAGCAAGGGCCTATGATTTAGCAGCTCTAAAGTACTGGGGTGCTTCTGCAACTACCAATTTCCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaattaattgatatatcgagtatggcaaatgatgtccatctttgattaattcaagGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
gattaat putative branch site (score: 3)
atctttgattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaagataatattctattgacaaattaattgatatatcgagtatggcaaatgatgtccatctttgattaattcaagGTGGATATGACAAGGAAGATAGAGCAGCTAGAGCCTATGACTTGGCAGCTTTAAAATACTGGGGTTCTACTGCTACTACAAATTTTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT