Sequence
atgc intronic sequence ATGC exonic sequencegttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 7
gttagctccccgacgcaaaactatatct-tcactgttatttaatataattggttacgttttctaggttg---tattcatctgatctttaaaggttggcgat-ttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
| | | | || | || ||| | || | || || | ||| || | |||| |||| || | || ||| || |||| |||||| ||| | || || ||||| |||||||| || ||||| |||||| |||||||||||||| |||||||||
------------attccaccccattcttctccttgtaggccattaacagtgaataaatgttcatggataaatcattcctctgttcactcgttcttcctatcatttatttcagGGAAACCAGGGTTTTCCAAGAAGCAAGCTGATCTCTTCTTCCCCCCAGATTTTCAGGATGATTTTCCTGTGGCCATGCAG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 7
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgtt-ttctaggttgtattcatctgatctttaaaggttggc------gatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
| | ||| | | || | ||||| | || | | | | || || ||| | | | || | |||| |||||||| || |||||||||||||| |||||||||||||| || |||||||| |||||||||||||||||||| ||||||||||||
--------------atagatatattctattatcactaaatcatatatataattctatcatctttgatttggttaatcatccttctggaatttaactttccaaatttctttgcagGGAAGCCATCATTTACAAAGAAACAAGCAGATCTTTTCTTTCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 7
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
| | | ||||| | | | | | |||| ||| || || ||| | | || | |||| |||| | |||| ||| |||| || ||||||||| | || |||||||||||||| || ||||| || |||||||||||||||||||| ||||||||||||
atagatatattgtattataactaaaccatttgtataattt--tatcatc--tttgatttggttaatc--atccttctggaatttatctttcca-aatttcttttcagGGAAGCCATCATTTTCCAAGAAACAAGCAGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 7
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgt-attcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
| | | | | |||| | | || | | || | || ||| | ||| | || ||| ||| ||| ||| |||| || ||||| | |||||||| ||||| || ||||| ||||| || || ||||| |||||||||||||||||||| ||||||||||||
--gaaatgttctatg--aaaccactcatgcatcttcacttcacctatcaacttaagcttttgcaatagttgttcccatgac----aaacattgctaatttgttggcagGGAGGCCATCATTCACAAAGAAGCAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 7
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
| | | |||| || || | | || | || ||| | ||| | || | || ||| || ||||| || ||||| || |||||||||||||| |||||||| ||||| || || ||||| |||||||||||||||||||| ||||||||||||
---ggaaacataatatgaaaccattcacacatcttcacttcacctatcaacttaagctttt---gccatagttggtccatgac-aaacattactgatttgttggcagGGAAGCCATCATTTACAAAGAAACAAGCTGATCTTTTCTTCCCCCCAGATTTTGCTGATGATTTTCCAGTTGCCATGCAG
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 7
-gttagctccccgacgcaaaactat-atcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
| || | | | || || || || || |||||| | ||| | | || || ||| ||||| ||| ||| || | |||| || ||||| |||||| ||||||||| ||||| || ||||| || ||||| || |||||||||||||||||||| ||||| ||||||
gactcactactcttggtggaatcattatgttaccttttattttgt---tttgaattctgttcttatgtt-tattc--ctgttct---aacttcaataatttcttagcagGGAAACCAGGATTTACAAAGAAACAGGCTGATCTTTTCTTTCCTCCAGATTTTGCTGATGATTTTCCAGTTGCAATGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
atctgat putative branch site (score: 4)
tttttttgc putative PPT
attttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctccccgacgcaaaactatatcttcactgttatttaatataattggttacgttttctaggttgtattcatctgatctttaaaggttggcgatttttttgcagGAAAACCATCATTTACAAAAAAACAAGCAGATCTCTTTTTTCCCCCTGATTTTGCTGATGATTTTCCTGTTGCCATGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT