Sequence
atgc intronic sequence ATGC exonic sequence...tccagatttaaactgttccattttttattgtacatctccgttttgcatttcgatcgtggactgtgttgattagggccacttatgtgttatgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15070.2 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 24
tccagatttaaactgttccattt--tttatt-gtacatctccgttttgcatttcgatcgtggactgtgttgattagggccacttatgtgttatgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
| || ||| | | || || |||||| || | | ||| | | || | | | | || || | || | || | |||| || | ||||| ||||| ||||| ||||| |||||||||||||| ||| ||||||| || ||||| || ||||||
tatagttttggattttttttgttagtttatttgtgtagattagttctctttgacgtttttaa--tattttcatcatagcttatctaacattg-attgttgtagCTTCTTGCTGATGGCGTAATTCCAAACGAGTATGGGATCAACCCAAAGCAAAAACTAAAAATTGGCTCAAAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GRMZM2G022997_T01 (Zea mays), 3'ss of exon 4
tccagatttaaactgttccattttttattgtacatctccgttttgcatttcgatcgtggactgtgttgattag--ggccacttatgtgtt-atgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
|| |||| | || | || | ||| | | | || | |||| | | | || |||| | || | || | || || | || || |||||||| || |||||||||||||||||||| ||| ||||||| || |||||||| ||||||
--caaatttgagctaatgtgttatagattccatgttctc-ttggacctttctttgtagtgtttctttaattatttgttatctgacacaccgatattcttctagATACTCGCTGATGGTGTTATTCCAAATGAGTATGGGATCAACCCAAAGCAAAAACTGAAAATCGGCTCAAAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 22
-tccagattt-aaactgttccattttttattgtacatctccgttttgcatttcgatcgtggactgtgttgattagggccacttatgtgttatgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
| |||| | |||| || || | || | | | | | | ||| | || || ||| || | || | |||||| ||||||| ||||||||||| |||||||| ||||| || |||||| |||| ||||| || || || ||||||
ctgcagaaatgaaacccttatatgtactacttttc-tgtgtatattgactgatgagttcaatct-cattgctttcctaattgctcagctaatttatttgcagATGCTTGCTGATGGTGTAATTCCAAATGAATATGGAATTAATCCAAAGCAGAAGCTGAAGATTGGCTCAAAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 38
-tccagatttaaactgttccattttttattgtacatctccgttttgcatttcgatcgtggactgtgttgattagggccacttatgtgtt------atgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
| |||| |||| | | ||||| || |||| || | || | || | | | | || || | || || |||||| ||||||| ||||||||||| |||||||| ||||| || | |||| |||| ||||| || || || ||||||
ctgcagaaataaa-------acccctatatgtactacttttctttgtatattgactgatgagttcaatctcattgctttcctaattgctcagctaatttgtttgcagATGCTTGCTGATGGTGTAATTCCAAATGAATATGGAATTAGTCCAAAGCAGAAGCTGAAGATTGGCTCAAAG
upper sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 24
tccagatttaaactgttccattttttattgtacatctccgttttgcatttcgatcgtggactgtgttgattagggccacttatgtgttatgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
|| | || | ||| | | || || | | | | | | ||| | | ||| || | || ||| ||||||||| |||||||||||||| |||||||||||||| || || || ||| |||| ||| | || || || ||||||
aatgcatatcaatcatcaaattacatctagttaccctttttgtaggctaaaggttgtgaccatttttgtaggctaagggttgtccattttgttgttgcagTTACTTGCAGATGGTGTCATCCCAAATGAGTACGGCATTAACCCAAAGCAGAAGTTGAAGATTGGATCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttcgatcgtggactgtgttgattagggccacttatgtgttatgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
tgttgat putative branch site (score: 4)
ttgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccagatttaaactgttccattttttattgtacatctccgttttgcatttcgatcgtggactgtgttgattagggccacttatgtgttatgtggttgcagTTGCTTGCAGATGGTGTAATCCCAAATGAGTATGGGATCAATCCACAGCAAAAGCTCAAAATCGGTTCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA