Sequence
atgc intronic sequence ATGC exonic sequence...atcgtgtttttgccttacttgagtacctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA15G04200.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 3'ss of exon 7
atcgtgtttttgccttacttgagtac-ctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
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----------------------gtatgctgcttacttcactcatttgaccttacattttcataatttctgtttcttactgtatttctgtt-------tcagATGGCGAGATGTCAAACTTCGGGCCTTTGATAATGCAAAGCACCGGACTTACGTTGATCTTAAG
upper sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G063151_T01 (Zea mays), 3'ss of exon 7
--atcgtgtttt-tgccttacttgagtacctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
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gtataatttcttgtacaccccccccccccttattcgacctgac-ataatttattgccttctgtatttctcactgtatagtta-----tggatatcatg--tagGTGGCGAGATGTTAAACTTCGCGCTTTTGACAATGCAAAGCACCGTACCTACGTTGACCTTAAG
upper sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g04940.t01 (Vitis vinifera), 3'ss of exon 8
-----atcgtgtttttgccttacttgagtacctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
|| | || || | | | | || || | | || || || | | | | ||| || ||||||||||||||| ||||| | ||||||||||||||||| || || || || || |||||||||
gactggatacagttaggaattggctgtgcagattttgtagttccataaatggtcttatgttacagcatgtcaagtttctaaccatatttccatcctg-----cagGTGGCGTGATGTGAAACTGCGAGCTTTTGATAATGCAAAACACCGAACTTATGTAGATTTGAAG
upper sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ13094 (Selaginella moellendorffii), 3'ss of exon 1
atcgtgtttttgccttacttgagtacctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
| ||||| | | ||||| | | || | | || ||| | || | ||||||||||||||| ||||| || |||||||| || || ||||| |||||||||| ||| | |||
---------------------------------gtaacgaagttttgtttcttgttttgttgtttctcttgacttatctcgtttggtcttttccttccagGTGGCGTGATGTCAAACTCCAGGCTTTTGAGAACGCCAAGCACAGGACATACGTGGATCTTAAG
upper sequence: GLYMA15G04200.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ14112 (Selaginella moellendorffii), 3'ss of exon 1
atcgtgtttttgccttacttgagtacctgggagat-ttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
||| | | | || || ||||| || || ||||| |||| | ||| ||| || ||||||||||||||| ||||| || |||||||| || || ||||| |||||||||| ||| | |||
----------------------gtaacaaagttttgtttcttgttttgttgtttctcttgac-------ttatctcgttggtcttttccttc------cagGTGGCGTGATGTCAAACTCCAGGCTTTTGAGAACGCCAAGCACAGGACATACGTGGATCTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
ttttgac putative branch site (score: 3)
tttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcgtgtttttgccttacttgagtacctgggagatttatttattttgcatttccttttgacaatccctttatatggtttccttttggctgtggaaatcagGTGGCGTGATGTTAAACTTCATGCTTTTGATAATGCAAAGCATCGGACATACGTCGATTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - -ttttgcc
- - - - - - - - - - - gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggctg