Sequence
atgc intronic sequence ATGC exonic sequence...tgctaaattttggaacttttaaccttagagatgataaatgtcgttgaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07590.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G33830.1 (Glycine max), 3'ss of exon 1
tgctaaattttggaacttttaaccttagagatgataaatgtcgttgaagttt--ttttttctttctatgtactaatcttcaat-gttatggatg-tgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
| | | || | || |||| || | | | || | || | | |||| | || | | |||| || | || |||||||||||||| |||||||| |||||||| || || ||||| || |||||||| |||||||| || || |||||||||||||| || ||||| || ||||| |
---tgtcatgcgctttttccatccgactcattgattaa-gctgcttaattccaattatctgcctctagttcctggtttgcaatcattctttttggcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGTGGTCTCTACAAAAAGCCAATGATAC
upper sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 1
tgctaaat-tttggaacttttaaccttagagatgataaatgtcgttgaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
|| | | | | | || | | | || | || | | | | | | | |||| | | | |||||||||||||| |||||||| |||||||| || || ||||| || |||||||| |||||||| || || |||||||| ||||| || ||||| |||||||| |
tgtcatgcacatattccatctgactcattgattaagctgcttatttccaattatctgcctctagttcatggtttgcaccaattctttttg-gcttatgcagGTTGTGCAGTTGTTTTCATGCTTAGACAAGATTAGCTATATTGAATGGGCCCTTGATTCTGAATATATTCTTTGCGGTCTCTACAAAAAGCCGATGATAC
upper sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 2
---tgctaaattttggaacttttaaccttagagatgataaatgtcgttgaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
|| |||| || |||| || | |||| | || |||| ||| || || || | | | || || | | || ||||||||||| || || || ||||| ||||| ||||||||||| || ||||||||||||||||| ||||| ||||||||||| ||||| | ||| ||||| |
ggatggtaaaccatgttcttttttgtttttt---ttttaaagatttttttttttttaatttgttggtaaataatgaaacttaaaattttattttctgatacagGTTGTGCAGTTATTCTCGTGCTTGGATAAGATAAGCTACATTGAGTGGGCTCTTGATTCAGAATACATACTTTGTGGTCTCTATAAGAGACCAATGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
tactaat putative branch site (score: 1)
ttttttttctttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctaaattttggaacttttaaccttagagatgataaatgtcgttgaagtttttttttctttctatgtactaatcttcaatgttatggatgtgaatgcagGTTGTGCAATTGTTTTCTTGCTTAGATAAAATAAGCTACATAGAATGGGCTCTTGATTCAGAGTACATTCTTTGTGGTCTTTATAAAAAACCGATGATTC
- - - attttgg
- - - - - - - - - - aacctta