Sequence
atgc intronic sequence ATGC exonic sequencegtatagattcttgaaagccataataagacttataaaacatttaaaagccgagttatctaaataacgatttttgtgagcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G17630.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G17630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G17670.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------------gtatagattcttgaaa----gccataat---aagacttataaaacatttaaaagccgagttatctaaataacgatttttgtga-gcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
||| | || || | ||||| ||||||| | |||| | |||| ||| || ||| | |||||| ||||||| ||||||||||| || | || || ||||||||||| || ||||||||||| || ||||| |||||| | | || || || || | |
gtattatataatatatcctatccactcatagtaacaaacactagttttctttggctcacacacacatatgtcttttaattgttgttataattaaaagacttttccttcattgttatatttgtttat--gaatcgttcttcttgcaatacagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTGATGGCTGTATATAAACCAGCTCGCA
upper sequence: AT3G17630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G04820.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------gtatagat-tcttgaaagccataataagacttataaaacatttaaaagccga-gttat-ctaaataacga------tttttgtga-gcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
| | || |||| || | | | | |||||||| | || | | ||||| | || || || ||| | ||||||| ||||||| ||||||||||| || | || || ||||||||||| || ||||||||||| || ||||| || ||| | |||| || || || | |
gtatatataatatatccattcatcataacaaacactgattttccttggctcacacacacatgtcttttaattgttgacataatttataaaagacttgtacttcattgttatatttgattgtgaatcttcttcttgcaatgcagGTGTTGAATGACCAAGCATTTGCCATTTGTGTTCTCATGGCATTGTTTACCACCTTCATCACCACCCCAATAGTAATGGCTGTTTATAAACCAGCTCGCA
upper sequence: AT3G17630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv05s0020g01150.t01 (Vitis vinifera), 3'ss of exon 2
--gtatagattc-----ttgaaagccataat--aagacttataaaacatttaaaagccgagttatctaaataacgatttt-----tgtgagcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
||| || || |||| | | || || | || | | |||| | | ||| | | |||||||||||||||| | ||||| |||||||| || ||||| |||||||| ||||||||||| || |||||||||| | || ||||| || || |
gtacataagctcactcattctggtacatagttgatgatttttggtctgggtaggtggctgaccatcttgcttccttgtttgattatatatatagGTGCTGAATGATCAGACTTTTGCTATCTTAGTTCTTATGGCGTTGTTCACCACCTTCATCACCACCCCAATTGTGACCGCCTTGTATAAGCCAGCCAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacttataaaacatttaaaagccgagttatctaaataacgatttttgtgagcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
aaataac putative branch site (score: 2)
tttttgt putative PPT
tataaaacatttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagattcttgaaagccataataagacttataaaacatttaaaagccgagttatctaaataacgatttttgtgagcagGTGCTGAATGATCAAGCATTTGCGATCTTAGTCCTAATGGCATTGTTCACAACCTTCATCACAACTCCAATTGTGATGCTTATTTACAAGCCTGCAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA