Sequence
atgc intronic sequence ATGC exonic sequence...tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46210.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 6
tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctgataatctttttt----acagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
| || | ||| || || |||| ||| | | || | || ||| | | | | || || | | || | ||||| ||||||||| || || ||| | ||||||||||||||||| |||||||| ||||| || |||||||||||||||||||| ||| | ||| | ||||| ||||
-aagcttttatgccaa-gta-atcattttacactcaaattgggatg-tttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 6
tagtgttgtttgctaa--tatatatcactttggataccaaatactctg-atttagcaagcatcccaaataatatacatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
| || | || || || | || | | || | | | | | | ||| || || | ||||||| | | | | ||||||||| || || ||| | ||||||||||||||||| ||||| || ||||| || |||||||||||||||||||| ||| ||||| | ||||| ||||
aaactttttatgtcaagtaatcatttacactcaaattgggatgtttggtgtatgatgtgacttgcaatcaactcac-tgttatgctatt--ttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 6
---tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagc-atcccaaataatatacatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
| | ||| | | ||| | | | | | ||| || | || ||| | | | ||| | | || ||||||||||| || ||| | ||||||||||||||||| |||||||| ||||| || || || || ||||| |||||||| |||||| || ||||| ||||
ttgtgaaatagttgtgatgtgcttttcaatccttgggttaggt-ttttatttttacatgtgatttgcaatcaactgacttctattttttc---ccccttgccagAACCGGCCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAAGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 6
tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctgataatcttttttac-agAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
||| | || | | | | ||| || ||| | || | | || | || || | | || | | || | ||||||| || ||||| | ||||||||||||||||| |||||||| ||||| || || ||||| ||||| |||||||| |||||| || ||||| ||||
atgtgcttttcgatcctcggcttatgtttttatttttc-tacatttatgtgagatttattttacatgcaatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 6
tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctg----ataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
|||| | ||| || | | | || | | || || | || || ||| | | || | || | | |||| | ||||||| || |||||||||||||| |||||| |||| |||||||| ||||||||||| |||||||| |||||||| || |||||| || ||||| ||||
---tgtttaaatttggattatttcttatggttcattgaacattact-ttcagtattagcccttaaaaattttaaactaagagtgtcttgtgcttcttttaatagAACCGACCTGCTGAGCTTATTGCAAAGTTTCTGGATGAGAAACTTCGTGCTGGGAACAAGGGTACATCTGAAGAGGAGTTGGAGGGTACACTTGATAAAG
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S143_152V6.1 (Physcomitrella patens), 3'ss of exon 6
tagtgttgtttgctaatatatatcactttggataccaaatactct-gatttagcaagcatcccaaataatat-acatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
| | |||||| | | | || | | || | | | | | | | ||| || || ||| | | | | ||||||||||| ||||||||||| ||||||||| | || | || || || ||||| |||||||| | ||| ||||| || ||||| | | ||||| ||||
-aattttgttttcaattggatttgagtt-acttgttatgtttccgagggtcgatgtcggtttggaattttaagactgattactgttgtgtggtggtgctcagAACCGGCCTGCTGAGCTTATCGCCAAGTTTATTGATGGAAAGCTGCGAGCTGGCAATAAGGGAATTTCAGAAGAGGAGTTGGAAGGCATCCTTGACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttagcaagcatcccaaataatatacatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
tgctgat putative branch site (score: 3)
tcttttttac putative PPT
aaataatatacatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - -caaatac
- - - - - - - - - - - - - - - - - - - - - - -gatttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaataa