Sequence
atgc intronic sequence ATGC exonic sequence...gcagttattcaataacaaattctagaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
Basic information
species | Glycine max |
transcript | GLYMA07G16510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G389416_T01 (Zea mays), 3'ss of exon 6
gcagttattcaataacaaattctagaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
|| | | || |||| |||| |||| | |||| | | | | | || ||| | | |||| || ||| || ||| ||| | || || || | || || ||||||| ||||||||||||||||||||| ||||||| || ||||| | || |||||| | || |||
---gtgagttctta-caaactctaactaatgaaaagctgacatt--ttccaaagataaatact-acatctgcaa----gagtac--cttttt-----cagGTTGCTGAAAATTTAATTCTTGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G472614_T01 (Zea mays), 3'ss of exon 3
gcagttattcaataacaaattctagaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
|| | | || |||| |||| |||| | |||| | | | | | || ||| | | |||| || ||| || ||| ||| | || || || | || || ||||||| ||||||||||||||||||||| ||||||| || ||||| | || |||||| | || |||
---gtgagttctta-caaactctaactaatgaaaagctgacatt--ttccaaagataaatact-acatctgcaa----gagtac--cttttt-----cagGTTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 6
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 9
gcagttattcaataacaaattctagaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
|| | | || |||| |||| |||| | |||| | | | | | || ||| | | |||| || || ||||| | ||| | || || || | || || ||||||| ||||||||||||||||||||| ||||||| || ||||| | || |||||| | || |||
---gtgagttctta-caaactctaactaatgaaaagctgacatt--ttccaaagataaatact-acatctgcaa----gagta----tcttt---ttcagATTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G552586_T01 (Zea mays), 3'ss of exon 1
----gcagttattcaataacaaattct-agaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
|| || | |||| | ||| | | | ||| | | ||| ||| | | | || | | || ||| ||| | || || || | || || ||||||| ||||||||||||||||||||| ||||||| || ||||| | || |||||| | || |||
atactcaaaagaacataggtgagttcttacaaactctaactaatgaaaagctgacattttccaaagataaatactacatctgcaagagtaccttttt-----cagGTTGCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAG
upper sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 1
gcagttattcaataacaaattct-agaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
| |||| | || | | | ||| | | ||| ||| | | | || | | | | | ||| ||| | | || || | || || ||||||| ||||||||||||||||||||| ||||||| || ||||| | || |||||| | || |||
--------------gtgagttcttacaatctctaactaatgaaaagttgacattttccaaagataaatactacatctgcaag-agtacctttt-----cagGTTTCTGAAAATTTAATTCTCGAGAAAACATCATGTCCTTTGGGTGTCCTATTGGTTATTTTTGAGTCCAGGCCTGATGCCTTGGTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
ttctgat putative branch site (score: 3)
ctgctcttt putative PPT
tcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcagttattcaataacaaattctagaaaatgttattaaaacatgcatcctattgctcaacactcattttggcaattctgattactgctctttgtgtccagCTAGCAGATAAACTCATCCTGGAGAAAATATCATGTCCTTTGGGTGTCCTCCTGGTTATATTCGAGTCTCGACCAGATGCCCTTGTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - -cctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctct