Sequence
atgc intronic sequence ATGC exonic sequence...tttatgcttgctgttctgcattgtttttggtgtgtcatgctcatatccttattccaaccttctgcacatgtttcttaccctgttcatcattgcattgcagATTTTTGTGTTGAGAGATTATGCAAGAGAAACTCTTTCTTTGAGATGGAGATCTTGGATGACAAGATATTACATTGATCGCTATCTGAAGAATCAAACTT
Basic information
species | Glycine max |
transcript | GLYMA08G17110.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g11946.2 (Oryza sativa), 3'ss of exon 3
tttat-gcttgctgttctgcattgtttttggtgtgtcatgctcatatccttattccaacct-tctgcacatgtttcttaccctgttcatcattgcattgcagATTTTTGTGTTGAGAGATTATGCAAGAGAAACTCTTTCTTTGAGATGGAGATCTTGGATGACAAGATATTACATTGATCGCTATCTGAAGAATCAAACTT
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tctatcaatcaaggatatgtactttctgtgttgcagaatcagca-acctgtattcctatgagtataattgtgttctgatttctgctc-tcactatactgcagTTCTTTGTCTTGAGAGACTATGCAAGGGAGACCCTTTCTTTAAGATGGCGATCTTGGATGACAAGTTATTACATGAAGCGCTACTTTAAAAATAGAACTT
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G074103_T02 (Zea mays), 3'ss of exon 3
tttatgcttgctgttctgcattgtttttggtgtgtcatgctcatatccttat-tccaaccttctgcacatgtt-tcttaccctgttcatcattgcattgcagATTTTTGTGTTGAGAGATTATGCAAGAGAAACTCTTTCTTTGAGATGGAGATCTTGGATGACAAGATATTACATTGATCGCTATCTGAAGAATCAAACTT
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catttgtttaatattct--agtgtcttctatttctgttcgtaaaaacctaatgttcttgtttttcaactcattgtatcaaaatttctttcgctgttatgcagTTCTTTGTCTTGAGAGACTATGCAAGAGAAACTCTTTCTTTGCGATGGCGATCTTGGATGACAAGTTATTATATGAAGCGTTACTTTAAAAACAGAACTT
upper sequence: GLYMA08G17110.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0085g01190.t01 (Vitis vinifera), 3'ss of exon 3
tttatgcttgctgttctgcattgtttttggtgtgtcatgctcatatccttat---tccaaccttctgcacatgtttcttacc--ctgt-tcatcattgcattgcagATTTTTGTGTTGAGAGATTATGCAAGAGAAACTCTTTCTTTGAGATGGAGATCTTGGATGACAAGATATTACATTGATCGCTATCTGAAGAATCAAACTT
|| | | | | ||| || | | |||| ||| | | | | | | ||| | ||| | || | ||| | ||| ||| |||||| | ||||||||||| |||||||| ||||||| |||| |||| ||||||||||||||||||||||| |||||||| || |||||||| |||||| || |
------ctaggcgattttcatagtatcattgggttcatattcagtttcatgtgcttttgatctttctaatttgtatattgcttgctgcattatctttgtcttgcagTTCTTTGTGTTGAGGGATTATGCCAGAGAAATTCTTGCTTTAAGATGGAGATCTTGGATGACAAGCTATTACATGGAACGCTATCTAAAGAATTGGACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttattccaaccttctgcacatgtttcttaccctgttcatcattgcattgcagATTTTTGTGTTGAGAGATTATGCAAGAGAAACTCTTTCTTTGAGATGGAGATCTTGGATGACAAGATATTACATTGATCGCTATCTGAAGAATCAAACTT
ttcttac putative branch site (score: 2)
tttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatgcttgctgttctgcattgtttttggtgtgtcatgctcatatccttattccaaccttctgcacatgtttcttaccctgttcatcattgcattgcagATTTTTGTGTTGAGAGATTATGCAAGAGAAACTCTTTCTTTGAGATGGAGATCTTGGATGACAAGATATTACATTGATCGCTATCTGAAGAATCAAACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - -gcttgct
- - - - - - -ttctgca
- - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - -catgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcacat