Sequence
atgc intronic sequence ATGC exonic sequence...gtctatctgtctatagtcgactggttttgtactaactatatacctgattgcatgtgacaatgttaaagaaagttatgaaggaaaatttccaattttacagGGATCATCGTGTACGAGTATGAACTGAAAATTGGATGGGGTAAAGCAGTTTCTCTACCGTCACAAGCATTACCCGCTCCACCACCTGGACATATGGCTAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G25060.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 8
--------gtctatctgtctatagtcgactggttttg--------tactaactatatacctga---ttgcatgtgacaatgttaaagaaagtta--tgaaggaaaatttccaattt--tacagGGATCATCGTGTACGAGTATGAACTGAAAATTGGATGGGGTAAAGCAGTTTCTCTACCGTCACAAGCATTACCCGCTCCACCACCTGGACATATGGCTAT
| ||| | || || || | | | | | | | | || || | ||| ||| ||| || | || | | || |||| | |||| | || ||||| || ||||||||||| ||||| ||||||||| | ||| |||| |||||||| || || || ||||| || || ||||| ||||| ||
gttagtgtgcacatccatgtagtgttaacccatctggataatgtttgttcattgtttatgggaacttgaaatgcttttttgtctgagattcttgccttcagcatatttgatgatttatttcagGTGTTATTGTGTATGACTATGAACTGAAGATTGGGTGGGGTAAATCTGTTGCTCTTCCGTCACAGGCTTTGCCTGCTCCTCCTCCAGGACACATGGCAAT
upper sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 7
---gtctatctgtctatagtcgactggttttgtactaactatatacctgattgcatgtgacaatgttaaagaaagttatgaaggaaaatttccaattttacagGGATCATCGTGTACGAGTATGAACTGAAAATTGGATGGGGTAAAGCAGTTTCTCTACCGTCACAAGCATTACCCGCTCCACCACCTGGACATATGGCTAT
| | ||| ||| | ||| | || | | || | | | | | | || | | | || | | || || |||| || | | || ||||| | | || || |||||||| |||| |||||||||||||| | |||||||| || ||||||||| |||| ||||| ||||| || || ||||| ||
ttcttttctctttcttttgtctcttttttctctcctgtatttgttcttttattaatataatcttcttt--gtttctgatcaaaaaaaaatttta-tgttccagGGGTAGTTGTTTATGAGTATGAGTTGAAGATTGGATGGGGTAAGTCTGTTTCTCTTCCATCACAAGCACTACCTGCTCCCCCACCAGGTCACATGGCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgcatgtgacaatgttaaagaaagttatgaaggaaaatttccaattttacagGGATCATCGTGTACGAGTATGAACTGAAAATTGGATGGGGTAAAGCAGTTTCTCTACCGTCACAAGCATTACCCGCTCCACCACCTGGACATATGGCTAT
acctgat putative branch site (score: 4)
aaaatttccaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctatctgtctatagtcgactggttttgtactaactatatacctgattgcatgtgacaatgttaaagaaagttatgaaggaaaatttccaattttacagGGATCATCGTGTACGAGTATGAACTGAAAATTGGATGGGGTAAAGCAGTTTCTCTACCGTCACAAGCATTACCCGCTCCACCACCTGGACATATGGCTAT
- ctatctg
- - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggaaa