Sequence
atgc intronic sequence ATGC exonic sequence...ttgtatatcttggtgcatgcaatgggtaaatgtgcttttgtattcatgcataatggaaaacctgagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
Basic information
species | Glycine max |
transcript | GLYMA08G03020.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03020.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 3'ss of exon 12
ttgtatat-cttggtgcatgcaatgggtaaatgtgcttttgtattcatgcataa--tggaaaacctgagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
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ttgtgcatacattttgtagctattaatttgat---tattaataatcttttatcatttgctaaatacatggttgatttattattcgtttgttcttacatgatagGCAACTCCTGATATGGCCGTGACTCTGCTTGAGATTGCTAGAATTTTTGCTACCAAAGTTCCTGGCAAGATCGATGCTGATGTACTACAACTCCTGTGGA
upper sequence: GLYMA08G03020.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G012319_T02 (Zea mays), 3'ss of exon 13
-ttgtatatcttggtgcatgcaatgggtaaatgtgcttttgtattcatgcataatggaaaacctgagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
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tttttatggttca-tgcacttatccttctgatttttattagcatgtgtccctttatctgatttcatgattgacttattattctgtttgtcttacatgatagGCAACCCCTGATATGGCTGTGACTCTGCTTGAGATTGCAAGAATTTTTGCCACTAAAGTTCCTGGAAAGATTGATGCTGATGTTCTACAGTTGTTATGGA
upper sequence: GLYMA08G03020.1 (Glycine max), 3'ss of exon 14
lower sequence: AT2G07360.2 (Arabidopsis thaliana), 3'ss of exon 15
-ttgtatatcttggtgcatgcaatgggtaaat-gtgcttttgtattcatgcataatggaaaacctgagtttgcttaatagttatttcaattttgctttga-agGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
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cttatccattgcgttgaaactgaagaaaaacttgttattgaggagtaatgt-taactgttttcttctgactagttaac--tctttttaatttttctttcacagGCAACTCCAGATATGGCTGTTATTCTTCTCGAAATTGCCAGAATATTTGCCACCAAAGTTCCAGGGAAAATTGACGCTGATGTCTTACAGCTGCTATGGA
upper sequence: GLYMA08G03020.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 3'ss of exon 15
--ttgtatatcttggtgcatgcaatgggtaaatgtgcttt-tgtattcatgcataatggaaaacctgagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
|||| |||| ||| | ||| || | | ||| | || | || | | | | | | | || || | || |||| |||| |||||||||||||||| ||||| ||||||||||||||||| |||||||| |||||||| || ||| ||||||||||||| |||||||| || ||||
taccatataaaatggtttttgcttccttt---tgtactgtgtatatacctggtttgtgtacttaatcaatattttattttctttttccttgttggcttattagGCAACTCCAGATATGGCTGTGACTCTCCTTGAAATTGCAAGAATTTTTGCTACTAAAGTTCCTGGGAAGATTGATGCTGATGTATTACAACTACTATGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcataatggaaaacctgagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
gcttaat putative branch site (score: 4)
ttttgcttt putative PPT
ttaatagttatttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtatatcttggtgcatgcaatgggtaaatgtgcttttgtattcatgcataatggaaaacctgagtttgcttaatagttatttcaattttgctttgaagGCTTCTCCAGATATGGCTGTTACTCTTCTTGAAATTGCAAGAATATTTGCTACCAAAGTTCCAGGAAAGGTTGATGCTGATGTGTTACAACTGCTCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - gcatgca
- - - - - - - - - - - - - - - - -gcttttg
- - - - - - - - - - - - - - - - - - - - - -tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacctga