Sequence
atgc intronic sequence ATGC exonic sequence...gatatttggattatcatcctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcctgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
Basic information
| species | Glycine max |
| transcript | GLYMA06G04210.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
gatatttggattatcatcctt-tgcaatttactaatattctctctagaagaaacttgcatttgagttgta--ttatgcctgactaga-ttaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
| || | |||| | ||| || | | | | | | ||| ||| ||| | | | | | |||| || | | | || |||| || | ||||||||||||||||||||||| || ||| |||| ||||||||| |||||| ||||||||||| | || || || |||| ||||
---agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaa-ttgtccctgattgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
upper sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 3'ss of exon 4
--gatatttggattatcatcctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcctgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
| ||| | | | | | || || || | |||| | | | | | || || ||||| | | | | | | ||| ||||||||||| | ||||||||||| ||||| |||| | || |||| ||||| ||||||||||||||||||| || | ||||| || ||||| || |
atcaaattgtgttcaatttgttgtgtggttgcctggtcttctttgatctatatgtatactttgctgtagtattctagaaaattg--tcatttgcgtttacagGTTGGTCCTCTAAGATGTTGGCCAGGTGGTCTGTGCTTATCTAGATCAATTGGGGATATGGATGTTGGTGAATGCATCATTCCTGTTCCTCATGTGAAAC
upper sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135444_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------gatatttggattatcatcctttgcaatttactaatattctc-tctagaagaaacttgcatttgagttgtattatgcctgactagattaatgatat---ttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
| ||||| ||| | | || || | | | || | | | || || | | | ||| || | ||| | | || ||||||||||| | ||||||||||| ||||| |||||||| || ||||||| || ||| | ||||||||||||| || | |||| || ||||| ||||
gttcgtgtctgtctcacccttaaccctgtgcgctcatgaatggattttgtgtgtgtttggcgtataacctcccattgtgtgtgtttggcgtataacctcctggtatagtttggtctccttgttttgtttgttctattatataacgtacattggagtaaacaggtttacctttttacatttcagGTTGGTCCTCTAAGATGTTGGCCAGGTGGTTTGTGTCTATCTAGATCCATAGGGGATCTTGATGTTGGTGAATGCATCATTGCTGTTCCTCATGTTAAGC
upper sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 4
--gatatttggattatcatcctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcctgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
|| || | || | || | | ||| | || | | | | ||| | || | || ||| | | || | || | || ||||||| | ||||||||||| ||||| || || |||||| |||| ||||||||| |||||| |||||||||||| | || || || |||| ||||
tggacatcttccataggttttcttttagagtcctattttttggtttgtagatgtgatccat--gccttcttttgatccttagttccttttttatccatccagATTGGTCCCCTTAGATGTTGGCCAGGTGGTTTATGCCTCTCAAGATCGATTGGTGATCAGGATGTAGGTGAATTTATTATTCCGGTTCCTTATGTGAAGC
upper sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
gatatttggattatcatc-ctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcc--tgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
| | ||| | | ||||| | | ||| | | | ||| | | ||| | | | |||| || | || ||| ||| |||||||| ||||||||||||||||||| ||||||||||| |||||||||| ||| |||||||||| |||| ||||| || || || |||||||||
aactgtcatattgtggtagctttgtagaatg-taacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatc--ttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
upper sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ12414 (Selaginella moellendorffii), 3'ss of exon 4
gatatttggattatcatcctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcctg-actagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
| || || | |||| ||| | | || | | ||| || | ||| | | |||||||| || |||||||||||||| || || | ||||| || | ||||||||||| ||||| || || || |||||||||||||| ||| | || || |
------------------------------------------gtgacttaagct--cttttgtgtttttctctgacaggactgaatgattgagctctatagGTTGGGCCATTGAGATGTTGGCCGGGAGGGCTTTGTCTTTCGAGGTCCATTGGTGACATGGACGTCGGGGAGTTTATTGTCCCTGTGCCATACGTGAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagaaacttgcatttgagttgtattatgcctgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
gattaat putative branch site (score: 3)
tagattaatgatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatatttggattatcatcctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcctgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC
- - - - - - - - -cctttgc
- - - - - - - - - - - - - - - - - - - - - - -gaagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcct
