Sequence
atgc intronic sequence ATGC exonic sequence...aatttggctttcctcaaaaaatttatctcctataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G62130.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
aatttggctttcctcaaaaaatttatctcctataatttagatgt-taacgttatggattggtggctt-cctaatcagtctgctcctgtacttct-ctac--acagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| | | | | | |||| || | | ||| || | ||| | | | || | | | ||| ||| ||| ||| |||||||| || ||||| | | ||||||||| |||| ||||| || ||||||||||| |||||||| ||||| ||||| ||||||||| |||| ||||| |
-----ctatattttgggacggatggagtattatatgttggctacctaattttctctatttaagtcctatcttaaaaattgcctctggtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
aatttggctttcctcaaaaaatttatctccta--taatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacac-agCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| || | || | ||| | | || | || || | | | | | | | | || | | | || |||| || |||| ||||| |||||| | | ||||| || |||| ||||||||||| |||||||| ||||| |||||||| || ||||||||||| |||| ||||| |
---atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
aatttggctttcctcaaaaaattt--atctcc-tataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| || || | | ||||| || || | ||| || ||| | || ||| | | ||| || ||| | | | ||||| || || || || || |||||||| || |||||||||| || || ||||||||||||||| | || || ||||||||||||||| |||||||||| |
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatctcgactctgaattaccttt-tgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 21
---aatttggctttcctcaaaaaatttatctcctataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
|| | | | | |||| | | | || | | || | | ||| | || | | | | ||| | || | ||||| || || || || || |||||||| || ||||||| || ||||| ||||||||||||||||| || || ||||||||||| || |||||||||| |
gtaaaaatcacaaacattaaaataatgtgaagttgtagcccatctcttgtcaaatt--attaatcatttttattttatgattgtgaattacct-tccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
aatttggctttcctca-aaaaatttatctcctataa---tttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtact--tctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| ||| ||| ||| | | | | | | ||| || | | ||| | | | | || | | || | || | | || | ||||| || || || || || |||||||| || ||||||| || ||||| ||||||||||||||||| || || ||||||||||| || |||||||||| |
-----agtaaaaatcacaaacattaaagtaatgtgaagttgtaggccttctcttgtcaaattattatcatttttat-attgtgattgtgaattgccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 17
aatttggctttcctcaaaaaattt--atctcc-tataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| || || | | ||||| || || | ||| || ||| | || ||| | | ||| | ||| | | | ||||| || || ||||| || |||||||| || |||||||||| || || ||||| ||||||||| | || || ||||||||||| ||| |||||||||| |
caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaat--attatccattctgttatctcaactttgaattaccttt-tgtgcagCCGTGCAAAGGAATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTCGCAAAGGCAATAGCTACTGAAGCTGGTGCAAACTTCATCAACATTT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
aatttggctttcctcaaaaaatttatctcctataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctaca-cagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| || || || || || | | || | | || |||||||||| || | ||||||||||| ||| | |||||||| |||||||||||||| ||||| || || || || |||||||| || ||||||| || |
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT
upper sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
aatttggctttcctcaaaaaatttatctcctataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctaca-cagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
| || || || || || | | || ||| || |||||||||| || | ||||||||||| ||| | |||||||| |||||||||||||| ||||| || || || || |||||||| || ||||||| || |
-----------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtctaacgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
tcctaat putative branch site (score: 2)
ctcctgtacttctct putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttggctttcctcaaaaaatttatctcctataatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacacagCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
aatttgg
- - - -ctttcct
- - - - - - - caaaaaa
- - - - - - - - - - - -tatctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggattgg