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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatgaaatgataatcaaattagtggcattagttcctgtattgatgttggatgtacacctccctcccctctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA

Basic information

species Glycine max
transcript GLYMA08G36700.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 5
----------------gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatgaaatgataatcaaattagtgg--catt-agttcctgtattgatgttgg--atgtacacctccctcccct-------ctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCTT--CAGGACCGAA
                  ||| |   |||| |      | | | |  || | | || | |  |     ||| | ||  || |    |       | || ||    ||| ||| |    ||||||  | |  | | |||  |  ||  |||        |||| ||||||||   || ||||| |||||||| ||||| || || ||||| ||||||||||||||||  ||  | |||||||  || || |  || ||   ||| | |   
gtagttattctgtaaataattgccagccttttgtcacctcttgcatatttagtttttaagcaaccgagcatgcaaatcattactacactgagttactactgaattattcagtacaaagattgatccttgaaacgcacaaatatcttacctgctgggattgttgtgcagGCATCTCAAGATCTGTCTTCCCTCAAGAATATGGCTGGAGAAACTGGAAAGAAGCTGACATCTATAGCCTCCAATTTTATCAGCGACCTCGACAGAATCC--

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G176612_T02 (Zea mays), 3'ss of exon 6
gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatgaaatgataatcaaattagtgg--cattagttcctgtattgatgttggatgtacacctccctcccctctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCT--TCAGGACCGAA
                                                               |    |  |  | ||| |  |||  |   | |   |||  |    ||||||||  |         ||   |||||| ||||   ||||||||| ||||| || ||| |||| ||||| |||||||||||||||||||  ||  |||||||||  || || |  || ||   ||||| |   
--------------------------------------------------------------gtagcctttttgt-aaactgttggatcggcaatctttgtggttcc-ttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC--

upper sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 6
---------------------------------------gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatg--aaatgataatcaaattagtggcattagttcctgt---attgatgttggatgtacacctccctcccctct----gttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA---
                                       |  |     ||| |    || ||  |       |   | |     |||  || |   |||   ||  ||   | || |||     ||     |  || |||   | |    |    |  |||    | |  ||| |    |||||| ||||   ||||||||| ||||| || ||| |||| || ||||||||||||||||||||||  || || |||||||  || || |  || ||   |||| |||   
gtaacttgttggcataacctgttgtttcttggaattttagcgtgtagcaccatagtttgcatacgttttaagccacaattgaactatgagttagcggaaacgtgctaaggaaaaaccaataccatgcagagacgtcgtgtgaaagttgcataaagtcaacagtctcatttcctgtcatggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAGAAGCTGACATCTTTCGCCTCCAATTTCATCAGCGACCT---GGACAGAATCC

Mapped 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|58017014|gb|CX703756.1|CX703756
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|193405135|gb|FK371658.1|FK371658
EST:     ATCTTACTGCTGGTGACCTCATCAATCGATTATC-TTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|298194738|gb|HO043210.1|HO043210
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|57575109|gb|CX548084.1|CX548084
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|22524808|gb|BU083619.1|BU083619
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTC
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTC
EST: gi|208268643|gb|GE069414.1|GE069414
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|58015077|gb|CX701819.1|CX701819
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|31311653|gb|CD396856.1|CD396856
EST:     ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATTGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcctta ... tgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattagttcctgtattgatgttggatgtacacctccctcccctctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA
             tattgat  putative branch site (score: 3)
                            tacacctccctcccct  putative PPT
             tattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattccttaccttgtactggatttggaaatttcattattcatgttatttgtcattcgaacaatgaaatgataatcaaattagtggcattagttcctgtattgatgttggatgtacacctccctcccctctgttttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTGAGCTCATTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA