Sequence
atgc intronic sequence ATGC exonic sequencegtctgttattatcttataataaaatttaaattatctatcaaaattacattccaaagtaagagagtggttacctgctactcaggaatattcatttctacatattcgccggccttaatttattttttcatttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
Basic information
species | Glycine max |
transcript | GLYMA17G12850.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 13
gtctgttattatcttataataaaatttaaattatctatcaaaattacattccaaagtaagagagtggttacctgct-actcaggaatattcatttctacatattcgccggccttaatttatttttt-catttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
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----------------------------------gtaccaaa--tac-ttataaaccaagcagttaatacttagcttgtctacacaaatgtagtgtaatgcagtaagcagacttgcagcattgctaatgccttgcatttcggagttgt---gataca------gATGGGAGGAAGAAACACCGTGCTGCTGGATGCAATAAGTTGGAGGATTCCTTTGGTCAGTGACATACCAACTATTATATTTGGTGCAGATGTCACGCATC
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 13
gtctgttattatcttataataaaatttaaattatctatcaaaattacattccaaagtaagagagtggttacctgctactcaggaatattcatttctacatattcgccggccttaatt-tattttttcatttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
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-------------------------------------------------------------------gtacttaccaccttgtt-tatacataaa-atacagtttagaacatcaactatataagtggctctattattgactaatggtaccaataaaattc-agATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGGATTCCGTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACATC
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 13
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 12
gtctgttattatcttataataaaatttaaattatctatcaaaattacattccaaagtaagagagtggttacct--gctactcaggaatattcatttctacatattcgccggccttaatttattttttcatttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
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------------------------------------------------------------gtacttaccaccttggttatacatcaa-atacagttcagaacagcaactt-tataagagaaatggctcgatattgactaatgataccatcaaat------tcagATGGGAGGAAGAAACACTGTGCTCCTGGACGCAATAAGTTGGAGCATTCCTTTGGTCAGTGACATCCCAACTATTATATTTGGTGCAGATGTAACACACC
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 13
gtctgttattatcttataataaaatttaaattatctatcaaaattacattccaaagtaagagagtggttacctgctactcaggaatattcatttctacatattcgccggccttaatttattttttcatttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
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--------------------------------gtctgtccagactg------aaacttctgtggcgatt--ctactacttaaaaata--gattgct---tatt--gcaaagttaatgtttcctctaagcttggtttcgggatttttc----tttttccccagATGGGTGGAAGAAATACTGTGCTTTTAGATGCTTTGAGTTCAGGAATTCCTTTGGTTAGTGACATTCCAACAATCATATTTGGAGCCGATGTAACTCATCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|26269315|gb|CA820378.1|CA820378EST: AGATCAATGTCAAG ATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCA
genomic: AGATCAATGTCAAGgtctgttatt ... atacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggccttaatttattttttcatttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
acttaat putative branch site (score: 4)
tactttt putative PPT
taatttattttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttattatcttataataaaatttaaattatctatcaaaattacattccaaagtaagagagtggttacctgctactcaggaatattcatttctacatattcgccggccttaatttattttttcatttttcacttaatatttccttaaatatacttttagATGGGAGGAAGGAACACAGTACTTTTGGATGCCCTAAGTTGGAGGATCCCATTGGTTAGTGACATTCCAACAATAATTTTTGGAGCAGATGTAACACATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG