Sequence
atgc intronic sequence ATGC exonic sequence...cccctagttcatggtgtgtgatttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
Basic information
species | Glycine max |
transcript | GLYMA06G06890.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 1
cccctagttcatggtgtgtgatttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatatttt--cttatttgtt---gctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
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----tgacccctgtgttactccttatcttggaaatgaacatgtc-attgtgtttttcacatggcagcccttcttgtggactctaacatacttctcttaattgcagACACATTATGTGTTGCTTCTTTGCTCATTCAAGGAACAACTTCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTGATGGGGTGCTGGGAACTTGAAC
upper sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
----cccctagttcatggtgtgtgatttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
| | ||| || || || | || | | |||| | | | || || || | || | | | | || ||| || ||||| |||| ||||| || | || ||||| ||||| |||||||| || || ||||| || || ||||||||||||||||| |||||||| ||||| | || |
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcc-taaggcaatttt---ttttacttaataaaaaaatgtttttttttcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
upper sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
cccctagttcatggtgt-gtgatttctg-atgtgatagagcttatctgctatgatacatttacaact--tacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
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---ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcgaatggttctaaattctaacctgtctcgtttttcgtc-cagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
upper sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 1
--cccctagttcatggtgtgtgatttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatattttcttattt-gttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
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tttgtctaggattccgtacatagttaacatcttgcatcatctgttttggccaggta---ttcctgttctcagattctaatatgtcactgttttattattacagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAACTCCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAAC
upper sequence: GLYMA06G06890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 2
cccctagttcatggtg-tgtg-atttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
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-tctttgtctagggttctgtacatagttaacatcttgcatcatctgtttttgccaggccttcttgttcccagattctaatatattcctgttt-ttattgcagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAGCTGCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAACMapped 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|105633903|gb|DW247266.1|DW247266EST: CCTTCGGACAAGCCATCGTTGGCGACGATAAAGAACTCGATCAGTTCTTG TCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCAT
genomic: CCTTCGGACAAGCCATCGTTGGCGACGATAAAGAACTCGATCAGTTCTTGgtattttcct ... gttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCAT
EST:
gi|105633102|gb|DW246627.1|DW246627EST: CCTTCGGACAAGCCATCGTTGGCGACGATAAAGAACTCGATCAGTTCTTG TCCCACTATGCTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCAT
genomic: CCTTCGGACAAGCCATCGTTGGCGACGATAAAGAACTCGATCAGTTCTTGgtattttcct ... gttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctatgatacatttacaacttacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
aacttac putative branch site (score: 2)
ttttcttatttgtt putative PPT
atacatttacaactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccctagttcatggtgtgtgatttctgatgtgatagagcttatctgctatgatacatttacaacttacaattttttatattttcttatttgttgctgcagTCCCACTATGTTCTGTTGCTCTGTTCTTTCAAAGAACAACTTCAACAGCATGTCCGGGTCCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGATCGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC