Sequence
atgc intronic sequence ATGC exonic sequencegtaatcttacctctactcgttttgttttcttaagatttgatttgatctgctggttgtttgtcacatttatgagaaattatttgatttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G37160.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G180811_T01 (Zea mays), 3'ss of exon 2
gtaatcttacctctactcgttttgttttcttaagatttgatttgatctgctggttgtttgtca--catttatgagaaattatttgatttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
||| ||| | || | | | | | |||| |||| ||| | | || | || ||| | |||||||| ||||||| || || |||||| |||||||| | |||||||||||| | ||||| || ||||||||||||||||| || |||||| || ||
gtagctccttttctcttgtgcatgcatgcatgttaagttgtttgtaactttggtatcctgtggttctctgatcacgtggtaattgcatcagGATCCAATAAAGTCCATCCACTTCAGCAGCTCAAACCCGCTTTGCCATGCATTTGACCCAGAGGCCAAGGATGGACATGATCTGCTCATTGGGGTGTTCT
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G096070_T01 (Zea mays), 3'ss of exon 2
gtaatcttacctctactcgttttgttttcttaagatttgatttgatctgctggttgtttgtcacatttatgaga------aattatttgatttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
||| || || | || |||| | | ||| | | | | | | | | | ||| | || ||| ||| ||||||||| ||||||| || ||| ||||||| |||||||| ||||||||||||| | ||||| || || || ||||| || || | |||||| || |
gtattcactattc-agtcattttactggaatg-gatgcaagccacacagtttttgatgtcttgcttttttctgatcatctgtttacttgcactagGATCCACTAAAGTCCATCCATTTCAGCAACTCAAACCCACTGTGCCATGCATTCGACCCAGAGGCCAAAGAGGGACACGACCTGATCATTGGGATGGGAT
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 2
gtaatcttacctctactcgttttgttttcttaagatttgatttgatctgctggttgtttgtcacatttatgagaaattatttg----atttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
| || | | || | ||| | | | || || ||| |||||| || ||| || |||||||| ||||||||||| || |||| |||||||| |||||||||||||||||| ||| ||| |||||||||| |||||| | | ||||| ||||
----------------gtataatgatcgggttagggtggatggattgtaaggatt-ttgactttattcatgagaggtttcttgttcaatgtagGATCCTGTAAAGTCTATCCACTTCAGTAATTCAAATCCTATGTGCCATGCATTTGATCAGGATTCTAAGGATGGGCATGATTTGATCATTGGCTTGAATA
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 2
gtaatcttacctctactcgttttgttttcttaagatttgatttgatctgctggttgtttgtcacatttatgagaaattatttg----atttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
| ||| || | || | ||| | | | || || | ||| | |||| || ||| || |||||||| ||||||||||| || |||| |||||||| |||| ||||||||||||| ||| ||| ||||||| || |||||| | | ||||| ||||
----------------gtatattggttgggttaggtg-gatggattgtatttatt-ttgattttattcacgagaggtttcttgttcaatgtagGATCCTGTAAAGTCTATCCACTTCAGTAATTCAAATCCTACGTGCCATGCATTTGATCAGGATTCTAAGGACGGGCATGATTTGATCATTGGCTTGAATA
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 2
gtaatcttacctctactcgttttgttttc--ttaagatttgatttgatctgctggttgtttgtcacatttatgagaaattatttgatttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
||||| | | | | || | | | ||| | || | || || | | | ||| ||| | | || ||| || |||||||| |||||||||||||| | || ||||| || ||| | || ||||||||| | || ||||||||||||||||||||| | ||||||||| |||| |
gtaatttgatgttttctggctgcggttttaatcaataattcatgtcttgcgttgg--aattggattttgagaggtttgttttttaatgtagGATCCCATAAAGTCTATACATTTTAGTAATTCGAATCCTGTTTGTCATGCATTTGACCCGGATGCTAAGGATGGACATGATTTGCTTATTGGGTTGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgatttgatctgctggttgtttgtcacatttatgagaaattatttgatttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
atttgat putative branch site (score: 5)
atttatgagaaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcttacctctactcgttttgttttcttaagatttgatttgatctgctggttgtttgtcacatttatgagaaattatttgatttagGATCCAGTAAAGTCTATACATATCAGCAATTCAAACCCTATGTGCCATGCATTTCATCCAGATGCTAAGGATGGACATGATCTACTTATTGGGCTGAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA