Sequence
atgc intronic sequence ATGC exonic sequencegtttgttttcgttgtttaaattgtggctacataaatcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G21270.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G32450.1 (Glycine max), 3'ss of exon 15
------------------gtttgttttcgttgtttaaattgtggctacataaat-catttttcata-atgtcatttcaaaatttag--taacaatggc-atatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
|||| ||| | || ||| | | | | | || |||| | | | | || | || | ||| ||| | | |||||| || || || || ||||| || || |||||||| || ||||| || ||||| ||| |||| |||||||||| |||||||| || ||||||||||||
gtatgataagctatgaaaatttgcattcctcattcaaaattaacttgctttgacatatacttcagatacatgaaccaaacttgtaatttgcttttggttgtatccattggcagCCATGTCTTGGTGGGGATTCCAAAACTTTGATGTTTGTGAACATCTCACCTGATCCATCTTCAACTGGAGAGTCACTTTGCTCTCTTCGGTTTGCTGCTG
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------gtttgttttcgttgtttaaattgtggctacataaatcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
| |||| || | || ||||| || |||| || || | ||||| || || |||| | |||||||| || ||||||||||| |||||||||||||| || ||||| || ||||| | ||| || || | || || ||| | || |||||||
gtgtgaccgccgttttacactggtttctgtgacatg--ctgcagctactgcaagcattcgagatttaagtgttcctgaatttgt--actttgt----tgctgtttcagCCTTGTCTCGGAGGAGATTCGAAGACCTTGATGTTTGTCAACATCTCTCCTGATATGAAGTCTTTGAATGAATCATTGTGTTCTCTCAGATTCGCTGCTA
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: PP1S80_62V6.1 (Physcomitrella patens), 3'ss of exon 15
------------------------------------------------------------------------------gtttgttttcgt--tgtttaaattg--tggctacataaatcatttttcataatgtcatttc--aaaatttagtaacaatggca-tatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
| | | | | | | ||||| || | | | || ||| || || | || | | || || | || || || | | || | |||||||||||||| ||||||||||||||||||||||| || ||||| |||||||| | || ||||| | ||||| ||| | || || || |
gtaaggcttctgaatgatgtgcgaatcggtcatcactatcgttctaatgcaaagtatataaataaacatgggtattgcatctaatattgcactccctgaattgagtgcgttaaaatattattattgttatttctcttactgacaacttgctgtcactgacaatttactgtttcagCCTTGCCTAGGGGGAGATTCAAAGACCTTGATGTTTGTCAACATCTCGCCTGATATGAAATCCTTGAATGAGTCCTTGTGCTCTCTCAGATTCGCAGCCA
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ35821 (Selaginella moellendorffii), 3'ss of exon 15
-------gtttgttttcgttgtttaaattgtggctacataaatcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGA--CCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
| | | | | || | || | | | || | | ||| | | | |||| | | | | | ||||||||||| |||| |||||||| ||||| |||||||||| ||||| | || || || | ||||
gtaaacaaagagatatggct-ttggactttgagttgcttagcgaggatcttatatgtactgagCGAGATTTTCTTCCCCTTTTTTTCATCT-TGCAGCCTTGCTTAGGTGGAGATTCGAAGACGCTGATGTTCGTCAACATCGCCCCCGAGGCCAAGTCGCTGC-----------------------------------
upper sequence: AT4G21270.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: EFJ36382 (Selaginella moellendorffii), 3'ss of exon 15
---------------gtttgttttcgttgtttaaattgtggctacataaatcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGA--CCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
| || | | | | || | || | | | || | | ||| | | | |||| | | | | | | ||||||||||| |||| |||||||| ||||| |||||||||| ||||| | || || || | ||||
gtaaacaaagagaggatatgatatggct-ttggactttgagttgcttagcgaggatcttatatgtactgagCGAGATTTTCTTCCCCTTTTTTTTATCT-TGCAGCCTTGCTTAGGTGGAGATTCGAAGACGCTGATGTTCGTCAACATCGCCCCCGAGGCCAAGTCGCTGC----------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
tagtaac putative branch site (score: 1)
ataatgtcatttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgttttcgttgtttaaattgtggctacataaatcatttttcataatgtcatttcaaaatttagtaacaatggcatatgcttgtgcagCCTTGCCTAGGAGGAGATTCAAAGACCTTGATGTTCGTAAACATTTCGCCTGACCCAACTTCTGCTGGAGAGTCTCTTTGCTCACTCCGGTTTGCTGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT