Sequence
atgc intronic sequence ATGC exonic sequence...acattagtttctttgagccaataccaagtcagaatggtccttttggtattgctaaactgttagtgtgtttcatatgaatctaataaatattataaaatagGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
Basic information
species | Glycine max |
transcript | GLYMA06G09860.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G09860.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G019153_T01 (Zea mays), 3'ss of exon 9
----------acattagtttctttgagccaataccaagtcag-aatggtcc---ttttggtattgctaaactgttagtgtgttt---catatg-aatctaataaatattataaaatagGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
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gtgagtttttcttttcttttaattgctacaattgcatttaagtaatattctaaatttctaattccctatactgtataactgtctatgtatatataatcatgttaaaataacttaacagGTGTCAGAGTAGAAGGGATCTTACGACAAGCTGCAGATGTTGAAGATGTTAAGCGTCGAATTCAGGAATATGAACAGG
upper sequence: GLYMA06G09860.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G24580.1 (Arabidopsis thaliana), 3'ss of exon 8
acattagtttctttgagccaataccaagtcagaatggtccttttggtattgctaaactgttagtgtgtttcatatgaatctaataaatattataaaat-----agGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
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--------------------gtattagtttca---ggttttttcagcttcttttgctgctttgttttactcactctgagctgataaagacaacaaaatcttgcagGAGTCAGGATAGAAGGAATCTTGAGACAAGCTGCTGATGTTGATGATGTTGAACACCGAATTCGCGAATATGAGAAAG
upper sequence: GLYMA06G09860.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv18s0001g07310.t01 (Vitis vinifera), 3'ss of exon 7
acattagtttctttgagccaataccaagtcagaatggtccttttggtattgctaaact-gttagtgtgtttcatatgaatctaataaatattataa---aatagGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
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---tcaaattgatgcaactgaaagtctctttctttaatggtgtagtcattgacatatttatttgtttgtttggt-tgaatatgattatttgagtaatttgacagGAGTCAAAATAGAAGGGATCTTGCGACAAGCTGCAGATGTCGATGATGTTGAATGTCGAATTCGGGAATATGAAAAAG
upper sequence: GLYMA06G09860.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 7
-----acattagtttctttgagc-----caataccaagtcagaatggtccttttggtattgctaa-actgttagtgtgtt--tcatatgaatctaata--aatattataa--------aatagGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
|||| | | |||||| || ||| | | ||| | | |||| | | |||| || | ||| ||||| | | | | | || ||| | | | | ||||||||||||||||| | || |||||||| || |||||||| || || || |||||||||||||
gtatgacatcc-ctccgttgagcatacttaaatgcaatccgcataggtgtatctattattccaattgctgtggaagtcacgattgaatggcactaattttagtgtctttattcgtatcaacagGCGTTGGCGTCGAAGGAATCTTGCGACAGTCCGCAGATGTTGAAGATGTTGAACGGCGTGTGCGTGAATATGAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattgctaaactgttagtgtgtttcatatgaatctaataaatattataaaatagGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
tgtgtttcatatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acattagtttctttgagccaataccaagtcagaatggtccttttggtattgctaaactgttagtgtgtttcatatgaatctaataaatattataaaatagGTGCTAACATAGAAGGAATCTTGCGACAAGCAGCTGATGTTGATGAGGTTGAACGTCGAGTTCGGGAATATGAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - caagtca
- - - - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - gctaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtt