Sequence
atgc intronic sequence ATGC exonic sequencegtattttagtgaacagattcattcatctctgtctttattacttgtccttaacatggttatcttttatatcagAAACTTGTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29880.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G53620.1 (Glycine max), 3'ss of exon 8
------------gtattttagtgaacagattcattcatctctg--tctttattacttgtcctta---------acatggtt-------atctttt-atatcagAAACTT-----GTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG-----------------
|||| | | || || ||| || | || | | || ||| |||| | ||| |||||| | |||| | | || ||||||||||| |||||||| |||||||| ||||||||||| |||| | || ||||||||| | |||
gtactgtgtagtgtataatgttaaaggagttgatttatttatggatgtacatgactggtcccttcaacttcctacacaaccctaaaaaatctttggacatcattgattgatttggttataactcctgtaaagAAAGAGCTGGGTCTGGCATTCAAGGGGAATCCGAGGATGGTGGTTGAAGCACATGAGGTAACTCTTCTCATGGT
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------gtattttagtgaacagattcattcatctctgtctttattacttgtcc--ttaacatggt-tatcttttatatcagAAACTTGTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG
| || || || || | || || | | || || || | | | || | ||||||| | || |||||||| || |||||||| |||||||| ||||||||||| || || | || ||||||||| | | |||
gtactgtttaatgcttaagatgttgatttgtttatgaatatacatgacttgtcccttcccttcaacttcatgctcaagcacaactctagaaaatatttggacatcactgattgacttgttctgtacattgtttcagAAATTGGTTATAACTCCAGTAAAGAAAGAGCTGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 6
---gtatttta-gtgaacagattcatt-catctctgt---ctttattacttgtccttaacatggttatcttttatatcagAAACTTGTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG
| |||| | |||| | | ||| | | ||| | || | || | | | | | | || |||||| | || ||| || | || ||||| |||||||||||||| |||| ||| |||||||||| ||||||||| ||||||||
gtaatgctttatgccaacatcatagcgatagttctatagacacgattgcatggc-ttgatgtt-tggtgtgtgattccagAAATTGGTTATAGCTACAGTAAAGAAGGAACTGGGTCTTGCTTTCAGGGGTAATCAAAAGATGGTGGTTGAAGCTTTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattcatctctgtctttattacttgtccttaacatggttatcttttatatcagAAACTTGTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG
ccttaac putative branch site (score: 3)
ttatctttt putative PPT
ttatcttttatatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttagtgaacagattcattcatctctgtctttattacttgtccttaacatggttatcttttatatcagAAACTTGTGATAACTCCTGTGAAGAAAGAACTGGGTCTTGCATTCAAGGGAAATCAAAAGAATGTGGTTGAATCTTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG