Sequence
atgc intronic sequence ATGC exonic sequencegtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
Basic information
species | Glycine max |
transcript | GLYMA08G28860.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
| | | | | | || ||| | | | ||||| ||| | | | | | |||| || | || | || | |||| |||| |||| ||||| ||||| || || ||||||||||||||||||||||| || |||||| | || ||||||||| ||||||| |||||||||||||
-------------------ggcaatagcttacgttctgcatgc--ggcttgtcaactttggacatt-gtacattatccaatttgaaataaatcaatattgtg----ccctcatcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
------------------------gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttata-atcacataacattcacacacacac---acacataccctgtac-------taatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
||||| | | ||||| | ||| | || | |||||||| | | ||| || | | | | || || | || |||| | | | | || | | ||| || |||| || || |||||||| || ||||||||||| ||||||||||| || |||||| | || ||||||||| ||||||| |||||||| ||||
gtcagaaaattattccaattgacgaagtgctactgcat-tgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgt-catctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgc--aattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
|| || || | |||| | | ||| || | | | | | | ||| || | ||| ||| | ||| |||| || ||||||| | ||||||||||||||||||||||||||||| ||||| || |||||| | || ||||| ||| ||||||| ||||||| ||||
----------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaa-acttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
| | | || | || | |||| ||| | | || | || || | || | || || || ||| |||| || | | | |||| ||| | || |||||||||||||| ||||| |||||||||||||||||||| || || || | || || || | ||| | |||||||| ||||
----------gtatgttcctgtgcccat-accttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatg---tgagaagattaactatagctgatacttctgt----gcagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
upper sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
------------------------------------gt-ctgctatggaaaatgatgatgacaatcaaaatgattg--ctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
|| | | ||||| | | | ||||| | || || ||| || || | |||| || || | ||| | ||| ||| |||| | | | | | ||| || |||| || || |||||||| || ||||||||||| ||||||||||| || ||||| | || ||||||||| |||| || |||||||| ||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgatcaacttatatggcttgccaaatttgtacttcgataaaatatccatctgga-acatggatg-tgtgctatc---ctgagctattttttcatcgtttttcagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
tactaat putative branch site (score: 1)
tactaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttataatcacataacattcacacacacacacacataccctgtactaatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC