Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaacctacttgaacctcagtaagttgttgcttttcccattcttaatgtgccttgttctatctgtagTGCTCTATACGTTGTTGACTTGGTTAAGTTCCGAGAGACAGCGGCAGGAGATAATCTAAGAGTATTCTATGAGACGCTTAGCAAGGATCCAAACAGTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71220.2 |
intron # | 34 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 34
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 34
gtaaaaaa--acctacttgaacctc--------agtaagttgttgcttttcccattct-----taatgtgccttgttctatctgtagTGCTCTATACGTTGTTGACTTGGTTAAGTTCCGAGAGACAGCGGCAGGAGATAATCTAAGAGTATTCTATGAGACGCTTAGCAAGGATCCAAACAGTTTG
|| | | || | ||||| || ||||||||| | | | | |||| || ||| | |||| || |||||| | || ||||||||| || |||||||||||||| || | ||||||||||| ||||| |||||||| || ||||||||||||||||| ||| |
gttagtgagtactttcttgattcttttgccaaaagtaagttggagttaattcagttctctgattattgtttccatttctgcttgcagTGCTTTGTATGTTGTTGACCTGAAGAAGTTCCGAGAGACTGCATCCGGAGATAATCTCAGAGTTTTCTATGAAACCCTTAGCAAGGATCCAAATAGTCTA
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 34
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 37
gtaaaaaaacctacttgaacctcagtaagttgttgcttttcccattcttaatgtgccttgttctatctgtagTGCTCTATACGTTGTTGACTTGGTTAAGTTCCGAGAGACAGCGGCAGGAGATAATCTAAGAGTATTCTATGAGACGCTTAGCAAGGATCCAAACAGTTTG
|| | || | || | | || | || |||| ||| | |||| | | |||||| |||| |||||||| || |||||||||||||| || || ||||||||||| ||||| | ||||| || || |||||||||||||| ||| |
gttagtggctactttttatattctattgccaaatataatttcaatgcttactgtttcaatttctgttttcagTGCTTTATATGTTGTTGATCTGAAGAAGTTCCGAGAGACTGCAGCTGGAGATAATCTTAGAGTTATATATGAAACACTAAGCAAGGATCCAAATAGTCTA
upper sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 34
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 35
gtaaaaaaac--ctacttgaacctca-------gtaagttgttgcttttcc--------------cattcttaatgtgccttgttctatctgtagTGCTCTATACGTTGTTGACTTGGTTAAGTTCCGAGAGACAGCGGCAGGAGATAATCTAAGAGTATTCTATGAGACGCTTAGCAAGGATCCAAACAGTTTG
||||| || | | | | || || | ||| | ||| || | | | || | || || |||||| |||| |||||||| ||||| || |||||||| || || || |||||||||||||| || |||||||| || || ||||||||||| |||||| |
gtaaataaccgatttcattaatttcttcatttcatggattgctagaattcttcgagaaagaactacagttctgacatgtggcatacttcctccagTGCTTTATATGTTGTTGATTTGGTGAAATTCCGAGAAACTGCAGCGGGAGATAATCTAAGGGTTTTCTATGAAACTCTCAGCAAGGATCCGAACAGTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacctcagtaagttgttgcttttcccattcttaatgtgccttgttctatctgtagTGCTCTATACGTTGTTGACTTGGTTAAGTTCCGAGAGACAGCGGCAGGAGATAATCTAAGAGTATTCTATGAGACGCTTAGCAAGGATCCAAACAGTTTG
tcttaat putative branch site (score: 3)
ccttgttct putative PPT
attcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaaacctacttgaacctcagtaagttgttgcttttcccattcttaatgtgccttgttctatctgtagTGCTCTATACGTTGTTGACTTGGTTAAGTTCCGAGAGACAGCGGCAGGAGATAATCTAAGAGTATTCTATGAGACGCTTAGCAAGGATCCAAACAGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG