Sequence
atgc intronic sequence ATGC exonic sequence...acttattaattgttacttatccattaatttatcagtcataactaatgaatatattacacgaattataaatttgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
Basic information
species | Glycine max |
transcript | GLYMA12G10520.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 6
--acttattaattgttacttatccattaatttatcagtcataactaatgaatata----ttacacgaattataaatttgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
|| | | |||| | | | | | | |||||| | | | | | | |||| | | | | | ||| | || ||||||| ||||||||| ||| | || ||||| |||||||||||||||||||| ||||| || ||| | || |
gtacaaagaacgtgttgcatttttcagtactcagtagtcatggttccttattttgattttggtttctgttattgacaaaacaactcactcattccatgtcttccagTGCTATATCAGGTGGAATTGTTGATAGAGCAATTGAAGCAGAGGACAGAAAACATGGTGACTTCATGAGAATT
upper sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132866_T02 (Zea mays), 3'ss of exon 4
-------acttattaattgt-tacttatccattaatttatcagtcataactaa---tgaatata-ttacacgaattataaatttgatatgtttttttttctcctt--tatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
| | | | | ||||| ||| || | | | | ||| | || || || | || | || | | || || | | | ||||||| ||||||||| ||| | || ||||| || |||||||||||||| |||||||| |||||| | ||| |
gtttgatggaaacagactctgtggctatcc-ttagttga-cgtttacaacgagttctggatttactcgtttcaaccgtgaaagtaactcaccttaagctccacgtgccttgcagTGCTATATCAGGTGGAATTGTTGATAGAGCAATCGAAGCAGAGGACAGGAAGCATGGGGATTTCATGAGGATA
upper sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------acttattaattgttacttatccattaatttatcagtcataactaatgaatatattacacgaatta---taaatttgatatgtttttttttctccttta----tctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
| | || | | | | | || || |||| || || | ||| | || | | | | | | |||| || | || | |||||| || | || || ||| ||||| || | |||||||||||||||| ||||||||||||||||| || ||
gtgagagtttgaatcttttagtataa--tgtcagatatcgaatcaaccacaatgttcttacatagtttctgagatgattcatactcagtgttaattttatttggcattggttctttagTGCCACGGCTGGCGGAATTCTAGACCGATCCATTGAAGCAGAGGACAAGAAGCATGGAGATTTCTTGAGATTG
upper sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 5
acttattaattgttacttatccattaatttatcagtcataactaatgaatatattacacgaattataaatttgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
| || | || || | ||| ||| || ||| | | | || | | | | | | | || || | |||||| || | || || ||| |||| ||||||| ||||| |||||||| ||||||||||||||||| || |||
----gtgaagttttgttt--tctttagttt-----------ctgatgtgagtttcattttggttctctgtatactgatgatgtgtgtcattgttctatagTGCCACGACCGGGGGAATTCTAGATCGAGCTATAGAAGCTGAGGACAGGAAGCATGGAGATTTCTTGAGACTG
upper sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 5
--acttattaattgttacttatccattaatttatcagtcataactaatgaatatattacacgaattataaatt-tgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
| ||| ||| || || | || | | ||| | || ||| || || ||| | | | | | |||| | | | | | ||||| |||||||| ||||| | ||||||||||| ||||||||||||| ||| |||||||| ||||| ||||||
ccttgtgttaccaacaactaatagatcatttgaataa-catgaata-tgag-atgataagtttattgcatactattaatcaaccttttgttttcatcactcagTGCCACATCAGGGGGTATACTGGACAGAGCTATCGAAGCAGAGGACAAAAAACATGGAGACTTCTTGAGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaatatattacacgaattataaatttgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
atttgat putative branch site (score: 5)
tatgtttttttttctc CT-rich tract
atattacacgaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acttattaattgttacttatccattaatttatcagtcataactaatgaatatattacacgaattataaatttgatatgtttttttttctcctttatctagTGCTACATCAGGTGGTATTTTAGACAGAGCTATTGAAGCAGAGGACAGAAAGCATGGAGATTTCTTAAGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - ccattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttacacg