Sequence
atgc intronic sequence ATGC exonic sequence...aagcttttatgccaagtaatcattttacactcaaattgggatgtttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
Basic information
species | Glycine max |
transcript | GLYMA08G10180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 6
aagcttttatgcc-aagtaatcat----tttacactcaaattgggatgtttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
|||| | | ||||| | |||| || | || | |||| |||| | | || | || | || ||||| | |||||| |||||||| || |||||||| |||||| | |||||||||||||| || || ||||| ||||| || ||||| || || |||| | | | |||||||
--ttttttgtacttaagtagatgtgtaatttatcctgcattttctttctttgtactatgttttattttatgaaagatcagct--caagcccttttttc-caacagAATCGACCTGCTGAATTGATTGCGAAGTTTCTTGATGAGAAACTTCGAGCTGGAAATAAAGGTACCTCCGAAGAAGAGCTGGAGGGAATATTGGATAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 6
aagcttttatgccaagtaatcattttacactcaaattgggatgtttggtgtatgatgtgact---tgcagtcaactcac-tgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
| | | | ||| | || | || | | | |||| || | | | || | | || ||| | | | | | ||||||||||||||| || |||||||| |||||| | |||||||||||||| || || ||||| || || || ||||| || || |||| || |||||||||||
---tgtctgttgtagctaaactttccattcttgg-tagagtagtttagttttttttttggttctatatgttcctgtcaaataatgggtcccatgcttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCGGAAGAAGAGCTGGAGGGTATACTTGATAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G704093_T02 (Zea mays), 3'ss of exon 6
aagctttta----tgccaagtaatcattttacactcaaattgggatgtttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccat-gacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
| ||| |||| | |||| | | || | || | ||| |||| | || || | | ||| | ||| | ||||||||| ||||| || |||||||| |||||| | |||||||||||||| || || ||||| || || || ||||| || || |||| | |||||||||||
---ttcttagaaatgcctgagggctgtcttactccacacatgtcagagtttttttat-atgttcttgtcaagtaa-tgggtcccatgtttgtttcatgtcaacagAACCGTCCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCAGAAGAAGAGCTGGAGGGCATACTTGATAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
-aagcttttatgccaa-gta-atcattttacactcaaattgggatg-tttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
| || | ||| || || |||| ||| | | || | || ||| | | | | || || | | || | ||||| ||||||||| || || ||| | ||||||||||||||||| |||||||| ||||| || |||||||||||||||||||| ||| | ||| | ||||| ||||
tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctgataatctttttt----acagAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
upper sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 6
aagcttttatgccaagtaatcatttta-cactcaaattgggatgtttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
| || || | || | || | | | | || || | | | | | |||| | || || | | ||||||||||||| ||| | ||||| |||||| ||||||||||||||||||| || || |||||||| ||||||||||| | |||| ||||||||||||||
-tgtttaaatttggattatttcttatggttcattgaacattactttcagtattagcccttaaaaattttaaactaagagtgtcttgtgcttcttttaatagAACCGACCTGCTGAGCTTATTGCAAAGTTTCTGGATGAGAAACTTCGTGCTGGGAACAAGGGTACATCTGAAGAGGAGTTGGAGGGTACACTTGATAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
aactcac putative branch site (score: 2)
ctatttttcc putative PPT
tattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagcttttatgccaagtaatcattttacactcaaattgggatgtttggtgtatgatgtgacttgcagtcaactcactgttatgctatttttccatgacagAACCGACCTGCAGAGTTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAATAAGGGTACTTCTGAAGAGGAACTAGAGGCTACACTTGATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - -tatgcca
- - - - - - - - - - - - - -cactcaa
- - - - - - - - - - - - - - - - - - - - atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg