Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttcaactttgagattaagtttgttacttatgttcttgatggaactttgtcttgttgtttattcgtttggtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G37160.2 |
intron # | 3 |
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 3
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 3
gtaatgttcaactttgagattaagtttgttacttatgttcttgatggaacttt--gtcttgttgtttattcgtttg---gtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
|||| | | || | | || ||| || || ||| | || ||| | || | || | ||| ||| || ||||||||||| | || ||| | |||||||| || |||||||||||||| ||||||||| | || |||||||||||||||||||||||||| ||||||||
gtaaaga--agtcttttgctaaaatttaacttttcattttgtgaggaaaatttaagcgttatgaatttattgttcctatgtgtatccttgtagTCTACTCAGTGTCATTGAGACAGCAATTACAGGATGTTGGTAAAAAGCTTGTTGGGGCCCAGCATTATAACAAAGATGGTTCTGTCAATAACAG
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 3
gtaatgttcaactttgagattaagtttgttacttatgttcttgatggaactttgtcttgttgtttattcgtttggtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
|||| || | | || || | || |||| | || |||| || | ||||||| | || || ||||||||||| ||| | || ||||| ||||| || || |||||||||||||| ||||||||| | || |||||||| |||||||||||||||
gtaactgaaaatgctttcactagaatttgaatttctgttttggaaggaaaatt---tatcaatttattcctatg-tgtattattgtagTTTACTCAGTGTCACTGAGACAACAATTACAGGATGTTGGTAAAAAGCTTGTTGGGGCCCAGCATTACAACAAAGATGGTTCT-----------
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 3
gtaatgttcaactttgagattaagtttgttacttatgttcttgatggaacttt----gtcttgttgtttattcgtttggtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
|||| || | | || || | || | || | | |||| || | | ||||||| | || || ||||||||||| ||| | || ||||| ||||| || || |||||||||||||| ||||||||| | || |||||||| ||||||||||
gtaactgaaaatgctttcactagaatttaaatttctattttggtaggaaaatttaaaatttatcaatttattcctatg-tgtattattgtagTTTACTCAGTGTCACTGAGACAACAATTACAGGATGTTGGTAAAAAGCTTGTTGGGGCCCAGCATTACAACAAAGATG----------------
upper sequence: AT2G37160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 3
--gtaatgttcaactttgagattaagtttgttacttatgttcttgatggaactttgtcttgttgtttattcgtt--tggtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
|| || |||| || || | | | || |||| ||| | || || | ||||| || || || |||||||| | || ||| | || ||||| || | ||| |||| |||||||||||| | || |||||||||||||||||||||| ||| |||| |||
gtaaaaaatttcactt-gattttgaatcaa--atttttgtttttggaagtttacactccatgaattgactcgttgtctttgtgtttttatagTCTACTCAGTGTCATTGAGGCAGCAATTACTAGATCTTGGGAAGAAGCTTGTTGGGGCCCAGCATTATAACAAAGATGGTTGTGTTAATAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgttcttgatggaactttgtcttgttgtttattcgtttggtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
tcttgat putative branch site (score: 4)
aattattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttcaactttgagattaagtttgttacttatgttcttgatggaactttgtcttgttgtttattcgtttggtgaattattgtagTCTACACCGTATCACTAAGACAGCAGTTGCAGGATGTTGGTAAGAAGCTTGTTAGTGCTCAGCATTATAACAAAGATGGTTCTGTAAATAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG