Sequence
atgc intronic sequence ATGC exonic sequencegttagctttgcacaatcttttttcttcagagttttgattttctttgttaaggagtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50310.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G36770.1 (Glycine max), 3'ss of exon 3
gttagctttgcacaatcttttttcttcagagttttgattttctttgttaag-gagtgtttgattatatagtcatatgataatgattggtttccatgtaaat----gcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG
|| | || || || ||| |||||| | ||||| | ||| || | || | ||| | |||| ||| |||||||| ||| || || ||||||||||| |||||||| ||||||| ||| ||||| || |||||||| || |||||||| ||||||||||| |||||||||
-----------------gttacgtgtttgaattgtg--tttatttgttgattgagtgatatgatatgtaccgagtgaattgttgttg-ccgcaatgtgaatttgtgcagACATTTGTGTACGGCGATCTCTACCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCAAGTCCGAATAGTCCTCCTCCTCGCAGTGCTCATCAAG
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G18170.1 (Glycine max), 3'ss of exon 3
gttagctttgcacaatcttttttcttcagagtt-ttgattttctttgttaag-gagtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG
|||| | | |||| || | | ||| ||| |||||| | ||||| | || | || | | | | | ||||||||| || ||||| ||||||| ||| |||||||| ||||||| ||| ||||| || ||||| || || || ||||| ||||||||||| |||||||||
gtta--caagtttgaactttcaactcaaacgcgattgcgtttatttgttgattgagtgcc--gtgatgtgaatgaattgttgttgccgcaatgtgaatttgtgcagACATTCGTGTATGGCGATCTCTTCCGGTATGATGTGGAGAAGCTGGAATGGAAATTGGTTTCCAGTCCTAACAGTCCTCCTCCTCGCAGTGCTCATCAAG
upper sequence: AT5G50310.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g10130.t01 (Vitis vinifera), 3'ss of exon 3
gttagcttt-gcacaatc----ttttttcttcagagttttgattttctttgttaagg---agtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG
|||| |||| | | ||| | | ||| | ||| || |||| || | | |||| | |||| | ||| || || |||| | ||||||| ||||||||||||||| || ||| ||||| | ||||||||||||||||| || | || ||||| ||||||||||||||||| || ||||||||||
gttaacttttgtataattgagacatgatgttctgtttttagagaatcttgatttgatgctaatctttgctcatatt-tggaatgtgtatatggaattgggatgt---ttcagACATTTGTATATGGTGATCTTTATCGACATGATATTGAGAAGCAGGAGTGGAAATTGATATCTAGCCCTAATAGTCCACCTCCTCGTAGTTCTCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggagtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG
gtttgat putative branch site (score: 5)
attatatagtcatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagctttgcacaatcttttttcttcagagttttgattttctttgttaaggagtgtttgattatatagtcatatgataatgattggtttccatgtaaatgcagACATATGTATATGGTGATCTCTACCGATATGATGTAGAGAAGCAGGAGTGGAAGTTAGTTTCAAGCCCCAATAGTCCACCTCCTCGCAGCTCTCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC