Sequence
atgc intronic sequence ATGC exonic sequence...aaactttttatgtcaagtaatcatttacactcaaattgggatgtttggtgtatgatgtgacttgcaatcaactcactgttatgctattttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
Basic information
| species | Glycine max |
| transcript | GLYMA05G27240.1 |
| intron # | 6 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 6
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 6
aaactttttatgtcaagtaatcatttacactcaaattgggat-gtttggtgtatgatgtgacttgcaat----caactcactgttatgctattttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
| | | | | ||| | ||| || || | | | |||| || | | | || | || | | | | | | | || ||||||||||||||| || |||||||| |||||| | |||||||| ||||| || || ||||| || || || ||||| || ||||||| || |||||||||||
----tgtctgttgtagctaaac-tttccattcttggtagagtagtttagttttttttttggttctatatgttcctgtcaaataatgggtcccatgcttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCGGAAGAAGAGCTGGAGGGTATACTTGATAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G704093_T02 (Zea mays), 3'ss of exon 6
aaacttttta----tgtc-aagtaatcatttacactcaaattgggatgtttggtgtatgatgtgacttgcaatcaactcactgttatgctattttcatat-gacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
|| ||| || | || | |||| | | || | || | ||| |||| | ||| || | | ||| | |||||| | ||||||||| ||||| || |||||||| |||||| | |||||||| ||||| || || ||||| || || || ||||| || ||||||| | |||||||||||
----ttcttagaaatgcctgagggctgtcttactccacacatgtcagagtttttttat-atgttcttgtcaagtaa-tgggtcccatgtttgtttcatgtcaacagAACCGTCCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCAGAAGAAGAGCTGGAGGGCATACTTGATAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
aaactttttatgtcaagtaatcatttacactcaaattgggatgtttggtgtatgatgtgacttgcaatcaactcac-tgttatgctatt--ttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
| || | || || || | || | | || | | | | | | ||| || || | ||||||| | | | | ||||||||| || || ||| | ||||||||||||||||| ||||| || ||||| || |||||||||||||||||||| ||| ||||| | ||||| ||||
tagtgttgtttgctaa--tatatatcactttggataccaaatactctg-atttagcaagcatcccaaataatatacatcttatgctgataatcttttttacagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
upper sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 6
-----aaacttt--ttatgtcaagtaatcatttacactcaaattgggatgtttggtgtatgatgtgacttgcaatcaactcactgttatgctattttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
||| || |||| || | | || || | || | || | | | | || || || | || |||| ||| | | ||||||||||||| ||| | ||||| |||||| |||||||||| |||||||| || || |||||||| ||||||||||| |||||| ||||||||||||||
tgtttaaatttggattatttcttatggttcattgaacattactttcagtattagcccttaaa---aattttaaactaagagtgtcttgtgcttctttta----atagAACCGACCTGCTGAGCTTATTGCAAAGTTTCTGGATGAGAAACTTCGTGCTGGGAACAAGGGTACATCTGAAGAGGAGTTGGAGGGTACACTTGATAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtatgatgtgacttgcaatcaactcactgttatgctattttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
aactcac putative branch site (score: 2)
ctattttc putative PPT
tattttcatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaactttttatgtcaagtaatcatttacactcaaattgggatgtttggtgtatgatgtgacttgcaatcaactcactgttatgctattttcatatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAGCTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTGGAGGCTACACTTGATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - tgtcaag
- - - - - - - - - - - - - -cactcaa
- - - - - - - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg
