Sequence
atgc intronic sequence ATGC exonic sequence...cctgatgtctagtcttcatttgactgagaatatgtttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtggctgctaatacagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
Basic information
species | Glycine max |
transcript | GLYMA06G10540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G150796_T02 (Zea mays), 3'ss of exon 6
cctgatgtctagtcttcatttgactgagaatatgtttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtggctgctaatacagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
|| || | | | | | | | | | | || | | | ||| ||| || ||| | |||| ||| |||||||||||||||||| |||||||||||||| || || || || || || | | | | |||||||| || ||||| ||| | ||||
-----------gtattaagatcttttatcaattatcatagtgcacaaaatatcccaaacacgta-----attctcaccacattttcgttctttaatctagACAGATCTTGTTATATATGAAATGAATGTCCGTGCCTTCACTGCCGACGAGTCAAGCAGGCTTGCTCCAGCTATTCGTGGAAGTTACCTTGGTGTCATTG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G385578_T01 (Zea mays), 3'ss of exon 4
cctgatgtctagtcttcatttgactgagaatatgtttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtggctgctaatacagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
| | ||| ||| | || || | || | | | || ||| ||| || ||| || |||| ||| |||||||||||||||||| |||||||||||||| || || ||||| || || | | | ||||||||| || ||||| ||| | ||||
--------------------gtattaagattatttatcataatgcactaaatatctcaaacgcgta---attgtcaccacatttttgttctttaatctagACAGATCTTGTTATATATGAAATGAATGTCCGTGCCTTCACTGCGGATGAGTCAAGCAAGCTTGGTCCAGCCATTCGTGGAAGTTACCTTGGTGTCATTG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G09020.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------cctgatgtctagtcttca------tttgactgagaatatg---tttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtg----gctgctaata-----cagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
| ||||| | | |||| ||||||| ||| | | || || | | | ||| ||| |||||| ||||||| | ||||| ||||||||||| ||||| |||||||| ||||| ||||| ||||||||| ||||| |||| || | ||||| ||||||||| | ||||
gtaaaaattgcatttgtttccttcagctagttgttgcacgattccgactttgaatatggaatttgtattcctgcagcatttatggtttctcccttattttgtttcagttttgtaatcagctgctactgttttgcagAAGGATCTTGTTATTTATGAAATGAATGTTCGTGCTTTTACTGCTGATGAATCCAGTGGGATGGACCCAGCTATAGGAGGCAGTTACCTCGGTTTCATTG
upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------------------------------cctgatgtctagtcttcatttgactgagaatatgtttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtggctgctaatacagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
| | ||| || | || | | || | | | | | | || || ||||||| || | |||||||||||||||||||||||||||||||| |||||||||||| |||| |||||||||| |||||| || | |||||||||||||| ||| ||||||
gtaatttagtggggcttaaatgcattatctcagttgtgacatgcaaaagaaattctttttctgcatatgttgtcctacgagatacaaatctgacagctctctctctctctctccccctccctcttcccccccactttccagtttgtgttttagttgtatatcttgacctt-attatttttgctattgtctttgcagAAAGATCTTGTTATATATGAGATGAATGTTCGTGCATTTACAGCTGATAAATCTAGTGGATTGGATCCAAATGTCCGTGGCAGCTACCTTGGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgaagtctaatgtatgctcttccattttcatcatttttgtggctgctaatacagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
tgctaat putative branch site (score: 2)
attttcatcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgatgtctagtcttcatttgactgagaatatgtttctggctgaatgaagtctaatgtatgctcttccattttcatcatttttgtggctgctaatacagAAAGATCTTGTTATATATGAGATGAATGTCCGTGCATTTACAAGTGATGAATCTAGTGGTTTGGATAGCAACATTCGTGGCAGCTACCTCGGTATGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- tgatgtc
- - - - - -gtcttca
- - - - - - - - - -ttgactg
- - - - - - - - - - - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtatg