Sequence
atgc intronic sequence ATGC exonic sequence...atggtcttacctttactctgtatacatgtaattatgagccacccttatattcacaactctagtttaattgtctattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
Basic information
species | Glycine max |
transcript | GLYMA07G40050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 3'ss of exon 5
atggtcttacctttactctgtatacatgtaattatga----gccacccttatattcacaactctagtttaatt-gtctattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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----ctttgagttcatgtcatgtataagatgtcttaaatatgtgatctttgcgta-acggatccatcccaattcattcgttgttttgtgaactaatgtaatacagCCTACTCTATGGAGCAGAAGATTCCTCGATTGCTGGAATGGTATTGGATAGTGCTTTCACTAACTTATATGGCTTGATGATGGAGCTTGTGGATGTCTAC
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 5
atggtcttacctttactctgtatacatgt--aat-tatgagccacccttatattcacaactctagtttaattgtctattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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-tagaagtacccctgtccataaaatattttaaatatttaggttctatttatgtattgaattttggt--aagttcttcataacttctgtccaaacttttgacagCCTACTGTATGGAGCAGAAGACCCCTCAATTGCCGGTCTGGTTTTGGACAGTGCTTTCTCTAACCTATATGACTTAATGATGGAGCTTGTAGATGTTTAC
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 5
atggt-cttaccttta-ctctgtata-catgtaattatgagccacccttatattcacaactctagtttaattgtctattcccttttactttg-gtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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-cggtacttgcatttaacgctgcaaaatatcttgatttaaattattcttga---tatatgtgcattttgatatttcatgacaatttgtgttatgtctgctgcagTCTGCTATATGGAGCAGAAGACCCCTCAATTGCTGGCATGGTTCTGGATAGTGCTTTCGCTAACTTATATGACTTAATGATGGAGCTTGTAGAAGTTTAC
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G081642_T04 (Zea mays), 3'ss of exon 5
atggtcttacctttactctgtatacatgtaattatgagccacccttatattcacaactctagtttaattgtctat--tcccttttactttggtgtga-tgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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-ccgctttaaaaaccatggtcaagcttgaaatatctcatcaccacttgatggctgtcccc--tttaattctttacaatattttgtatacaaatgtaaatacagCCTACTCTATGGAGCAGAGGACCCTTCTATTGGTGGCATGATATTGGATAGTGCCTTCACTAACCTGTATGACTTGATGATGGAACTTGTTGACGTTTAC
upper sequence: GLYMA07G40050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------atggtcttacctttactctgtatacatgtaattatgagccacccttatattcacaactctagtttaattgtctattcccttttactttg-----gtgtgatgt--agTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
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gttacttcttgagctacttttcagtcacacttaaaagtagtattagtagttgtgttgactatagattcaccagctttctaaaggtctatgatctgaaaagtgtgtcaactctccacatttcatcttgttctctccatcatttgatgaagcgggaatataatgtgcagCCTTCTCTATGGAGCAGAAGATCCTTCAATTGCTGGAATGGTCCTAGACAGTGCATTTTCAAACTTATTTGATCTGATGATGGAACTAGTGGATGTCTACMapped 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|208104844|gb|GD907341.1|GD907341EST: CAAATATCTTGTATGGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG TCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAG
genomic: CAAATATCTTGTATAGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAGgtattacatc ... tgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAG
EST:
gi|193727548|gb|FK664472.1|FK664472EST: AAATATCTTGTATAGGTCTTTGGGGGACGATCAATGGGTNCTGTTACTAG TCTTCTTTATGGAGCTGAAGACCC
genomic: AAATATCTTGTATAGGTCTTTGGGG-ACGATCAATGGGTGCTGTTACTAGgtattacatc ... tgtgatgtagTCTTCTTTATGGAGCTGAAGACCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattcacaactctagtttaattgtctattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
gtttaat putative branch site (score: 4)
tttaattgtctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atggtcttacctttactctgtatacatgtaattatgagccacccttatattcacaactctagtttaattgtctattcccttttactttggtgtgatgtagTCTTCTTTATGGAGCTGAAGACCCTTCTATTGCTGGAATGGTGTTGGATAGTGCCTTTTCGAACTTATATGATCTCATGATGGAGCTTGTGGATGTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT