Sequence
atgc intronic sequence ATGC exonic sequence...acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactagattaatttgtatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
Basic information
species | Glycine max |
transcript | GLYMA17G36150.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 3'ss of exon 4
--acacttttgtttaggtt-ttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactagattaatttgtatc-aaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
| || |||| | || |||| || | || | | || | | | || | | || ||| | || | | ||||| | | ||||||||||| | ||||||||||| |||||| |||| | || |||| ||||| ||||||||| ||||||||| || | ||||| || |||| || |
atcaaattgtgttcaatttgttgtgtggttgcctggtcttct----ttgatctatatgtatactttgctgtagtattctagaaaattgtcatttgcgtttacagGTTGGTCCTCTAAGATGTTGGCCAGGTGGTCTGTGCTTATCTAGATCAATTGGGGATATGGATGTTGGTGAATGCATCATTCCTGTTCCTCATGTGAAAC
upper sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactaga---ttaatttgtatc---aaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
|| ||||| ||| | | | |||| | | || || | |||| ||| |||| | | | || ||| || || || | || | || |||| || | ||||||||||||||||| ||||| || ||| |||| ||||| ||| |||| | ||||||||||| | || || || ||||| ||||
---agttagtttatgttgtacatgc-tgttgattgttgaaaggttcatagaaaattgtccctgat--tgacacctcttacttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC
upper sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G135444_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------------------------acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactagattaatttgtatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
| || || | |||| || | |||||||||| |||||| | || || | || | || | | | || ||| || ||||||||||| | ||||||||||| |||||||||||||| || |||| || || ||| | ||| ||||||||| || | |||| || |||| ||||
gttcgtgtctgtctcacccttaaccctgtgcgctcatgaatggattttgtgtgtgtttggcgtataacctcccattgtgtgtgtttggcgtataacctcctggtatagtttggtctccttgttttgtttgttc-tattat--ataacgtacat-tggagtaaacaggtttacctt------tttacatttcagGTTGGTCCTCTAAGATGTTGGCCAGGTGGTTTGTGTCTATCTAGATCCATAGGGGATCTTGATGTTGGTGAATGCATCATTGCTGTTCCTCATGTTAAGC
upper sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 4
---acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactagattaatttgtatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
||| || |||||||| | | || | ||| | || | || | | | || || | | | || | | ||| | | ||||||| | ||||||||||| |||||||| || |||||| |||| ||||| ||| |||| | |||||||||||| | || || || ||||| ||||
tggacatcttc-cataggttttcttttagagtcctattttttggt-ttgtagatgtgatccatgccttcttttgatccttagttccttttttatccatcca-gATTGGTCCCCTTAGATGTTGGCCAGGTGGTTTATGCCTCTCAAGATCGATTGGTGATCAGGATGTAGGTGAATTTATTATTCCGGTTCCTTATGTGAAGC
upper sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G052699_T02 (Zea mays), 3'ss of exon 4
acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatg-cctg-actagattaatttgtatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
|||| | | | | || | |||||| ||| | ||| | | | || | | | || ||| | | ||| ||| || | | |||| || | |||||||||||||| |||||||| || ||| | || ||||||||| ||| ||||||||||||| || || || || ||| ||||
acaccatgggcaggtgatggttttggagttttggttaattgctct-ttgtatattttttctttccacttgcttgacctatatttaatttttttacctcca-gATTGGCCCCCTTAGATGTTGGCCTGGAGGTTTGTGCCTATCAAGGTCAATTGGAGATCAAGATGTTGGTGAATTTATCGTTCCAGTTCCTCTTGTGAAGC
upper sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatg-----atattaatatgcctgactagattaatttg--tatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
| | |||| | || | || | | ||| | ||| || | ||| | | | || | ||| | | | || |||||||| |||||||||||||||||||| ||||||||||| |||| ||||||||| ||||| |||| |||| ||||| || || || ||||||||||
-------aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaaaaagtgtttatgatattaatatgcctgactagattaatttgtatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
aaaagtgtttatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatgatattaatatgcctgactagattaatttgtatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - -ggttttg
- - - - - - - - - - - -tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - gaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgcct