Sequence
atgc intronic sequence ATGC exonic sequencegttagctatttcgattttgtgtttatgatctcgaagattgttattaaaatgtatcggttttatgaattgtgggtatgagaaattatgagtaaactacatgctagttcaaccatcattactctaaatttgtgatttttttctgaaaattagattatgtgatgtgtagTGTTGGAATGGAGGTGGTGATGGTGTAGCAACTGCAACCATCATGGTTCTTGGTGATACTTGTACTCGTGGCTGTAGATTCTGTGCTGTTAAAACAAGTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08415.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G42600.1 (Glycine max), 3'ss of exon 2
gttagctatttcgattttgtgtttatgatctcgaagattgttattaaaatgtatcggttttatgaattgtgggtatgagaaattatgagtaaactacatgctagttcaaccatcattactctaaatttgtgatttttttctgaaaattagat-tatgtgatgtgtagTGTTGGAATGGAGGTGGTGATGGTGTAGCAACTGCAACCATCATGGTTCTTGGTGATACTTGTACTCGTGGCTGTAGATTCTGTGCTGTTAAAACAAGTA
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--------------------------------------------------------gttttatt--ttattattttttaaaattcttt-tgcattccctcttcccttctcccttgg-attcttatttattgttgagctttggattgttatgtgtgtgtg-tggacagTGTTGGAATGGAGGCGGAGATGGCATTGCAACTGCGACAATCATGGTTCTTGGGGATACTTGCACGCGTGGGTGTAGGTTTTGTGCTGTGAAGACCAGCA
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G24430.1 (Glycine max), 3'ss of exon 1
gttagctatttcgattttgtgtttatgatctcgaagattgttattaaaatgtatcggttttatgaattgtgggtatgagaaattatgagtaaactacatgctagttcaaccatcattactctaaatttgtgatttttttctgaaaattagattatgtgatgtgtagTGTTGGAATGGAGGTGGTGATGGTGTAGCAACTGCAACCATCATGGTTCTTGGTGATACTTGTACTCGTGGCTGTAGATTCTGTGCTGTTAAAACAAGTA
| |||| | ||| || | || | || || || | | | |||| |||| || | || | | |||| || ||||||||||||||||||| ||||| | |||||||| || |||||| ||||||| |||||||| || ||||| ||||| || |||||||| || || || |
------------------------------------------------------------aaggaatcgcacccgtgaccttttccctcttcccttctcccttgtattgttatttgttgttgagctttg-gattgttatgtgtgtgtg----tgtgtg-tggacagTGTTGGAATGGAGGTGGAGATGGCATTGCAACTGCGACAATCATGCTTCTTGGGGATACTTGCACACGTGGGTGTAGGTTTTGTGCTGTGAAGACCAGCA
upper sequence: AT5G08415.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0071g01020.t01 (Vitis vinifera), 3'ss of exon 1
gttagctatttcgattttgtgtttatgatctcgaagattgttattaaaatgtatcggttttatgaattgtgggtatgagaaattatgagtaaactacatgctagttcaaccatcattactctaaatttgtgatttttttctgaaaattagattatgtgatgtgtagTGTTGGAATGGAGGTGGTGATGGTGTAGCAACTGCAACCATCATGGTTCTTGGTGATACTTGTACTCGTGGCTGTAGATTCTGTGCTGTTAAAACAAGTA
||| ||| | || || | | || | ||| || |||| ||| | | || |||| | | | | || || | |||| |||| ||||||||||| || ||||| | ||||||||||| |||||| ||||||| ||||| || ||||||||||||||||| |||||||| ||||| ||||
--------------------------------------------------------atttagtgatctctga-----aggagtagtggagggatgttatgg-agccaaaccttcagaaattggg---tggaatttctgtatttatctttaggaatttt-tgtgcagTGCTGGAATGGAGGCGGGGATGGCATTGCAACTGCAACAATCATGCTTCTTGGGGATACCTGCACTCGTGGCTGTAGATTTTGTGCTGTGAAAACCAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcattactctaaatttgtgatttttttctgaaaattagattatgtgatgtgtagTGTTGGAATGGAGGTGGTGATGGTGTAGCAACTGCAACCATCATGGTTCTTGGTGATACTTGTACTCGTGGCTGTAGATTCTGTGCTGTTAAAACAAGTA
ctctaaa putative branch site (score: 3)
taaatttgtgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctatttcgattttgtgtttatgatctcgaagattgttattaaaatgtatcggttttatgaattgtgggtatgagaaattatgagtaaactacatgctagttcaaccatcattactctaaatttgtgatttttttctgaaaattagattatgtgatgtgtagTGTTGGAATGGAGGTGGTGATGGTGTAGCAACTGCAACCATCATGGTTCTTGGTGATACTTGTACTCGTGGCTGTAGATTCTGTGCTGTTAAAACAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT