Sequence
atgc intronic sequence ATGC exonic sequence...atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
Basic information
species | Glycine max |
transcript | GLYMA10G32500.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 9
-----------atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
| || | | || || | |||| |||| | || | || | | || | | || | | ||||| || || | | || ||||| || || ||||| | ||||||||||| | | || | | ||||||||| || || ||||||||||| ||||| ||||||||||||||||| |||
ttgcctattgagttttgccttacagtggctttaatattgtagtat--attttacaactaattatgttact----gtattcattgaacatatg-----aaccaattttacagGTTTAAGTGTATTGACCTTGATGGAAATGGCATTTTAACCACCACTGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAA
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 9
atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaac--atttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
| || | | | | | | | | || | | | || | | | | | | | | | | | | | | | | || || | | | ||||| || ||||| ||| | ||||| ||||| | | || ||||||||||| || || || |||||||| ||||| || |||||||||||||| |||
gttgttgtgatctattaccttattctatctttgcta--tacacattgtatatctcaggttacagttgtatttttattgaaatatgggaaacaactttcgcagGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTTCAATGAAATGCAATTTTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAA
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S147_62V6.2 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------atatttctagattgtaaattcagtatttcagtagcaagttcagaattt----------gatttgctgcatt-taatagaaac-tcaac----atttgttttta-----aaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
|| | || || |||||||| | | | | | ||| |||| | | ||| || || || | |||| ||||| | | | || ||||||||||| | || ||||| | |||| ||| | ||||||||||| ||||| | |||||||||||||| | |||||||||||||||||||| ||
gtacgtacctttatatggcctctaaaatgctctccacttttttggcatgaagttgatgtttttgaatgcaaatcatgtgctttctgacaaaacagtatttaggataaaggattgaattttcactcggattgattagttacataacaacgaggacatcgagtctaatttattttttcttgtacacctgatgcagGTTCAAATGTGTGGACCTGGATTGTGATGGTGTGATAACACCAAATGAGATGCAATATTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAG
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 9
atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
| | || | || || | | || || | | | ||| ||||||||||| || ||| ||||| | | |||||| |||| ||||| || ||||||| |||||| |||||||| |||||||| ||||||||| | || |||
------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTACGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA
upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
| | || | || || | | || || | | | ||| ||||||||||| || ||| ||||| | | |||||| |||| ||||| || ||||||| ||||||||||||||| |||||||| ||||||||| | || |||
------------------------------------------gtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
atttaat putative branch site (score: 4)
ttcttgt putative PPT
atttaatagaaactca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatttctagattgtaaattcagtatttcagtagcaagttcagaatttgatttgctgcatttaatagaaactcaacatttgtttttaaaaattcttgtagGTTCAAATGCATTGATTTGGATGGAAATGGAGTGCTGACACCAAATGAAATGCAGTTCTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcaaca