Sequence
atgc intronic sequence ATGC exonic sequence...atcgtgtttttgccttacttgagtattgggagatttatttattttgcatttcctttttgacaatccctttatatagtttccttttgggtgtggaaatcagGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA13G41210.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 7
atcgtgtttttgccttacttgagtattgggagatttatttattttgcatttcctttttgacaatccctttatatagtttccttttgggtgtggaaatcagGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
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--------------------gtatgctgcttacttcactcatttgaccttacattttc-ataatttct-------gtttcttactgtatttctgtttcagATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG
upper sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G063151_T01 (Zea mays), 3'ss of exon 7
-------atcgtgtttttgccttacttgagtattgggagatttatttattttgcatttcctttttgacaatccctttatatagtttccttttgggtgtggaaatcagGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
|| ||| || | |||| | | | || ||| || | || || || | | ||||||| ||| | | |||||||| |||||||||||||| || ||||||||||||||||| || || ||||| || | |||
gtataatttcttgtacaccccccccccccttattcgac--ctgacataattta---ttgccttctgtatttctcactgtatagtta-----tggatatcatg--tagGTGGCGAGATGTTAAACTTCGCGCTTTTGACAATGCAAAGCACCGTACCTACGTTGACCTTAAG
upper sequence: GLYMA13G41210.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G110309_T01 (Zea mays), 3'ss of exon 8
atcgtgtttttgccttacttgagtattgggagatttatttattttgcatttcctttttgaca--atc------cctttatatagtttccttttgggtgtggaaatc----agGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
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---------------------------gtatagtttatttattccactcgttcgacctgacagaatttcatggcttctgtattctcactgtatggttatggatatcatgtagGTGGCGAGATGTTAAACTTCGCGCGTTTGACAATGCGAAGCACCGTACCTATGTTGATCTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatttcctttttgacaatccctttatatagtttccttttgggtgtggaaatcagGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
ttttgac putative branch site (score: 3)
tttatatagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcgtgtttttgccttacttgagtattgggagatttatttattttgcatttcctttttgacaatccctttatatagtttccttttgggtgtggaaatcagGTGGCGCGATGTTAAACTTCGTGCATTTGACAATGCAAAGCATCGGACATACGTGGATTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - -ttttgcc
- - - - - - - - - - - - -ttgggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgggtg