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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctttaccttttactggatttgggaatttcattattcatgtcatttgtcatctgaacaacaaaatgataattgaattagtgacattagtttctgtattcatgttggatgggttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA

Basic information

species Glycine max
transcript GLYMA01G12340.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G176612_T02 (Zea mays), 3'ss of exon 6
gtattctttaccttttactggatttgggaatttcattattcatgtcatttgtcatctgaacaacaaaatgataattgaattagtgacattagtttctgtattcatgttggatgggttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCT--TCAGGACCGAA
                                                                       ||      ||    ||  | |  || | | || |  ||| |   | | |||            ||   || ||| ||||   ||||||||| ||||| || ||| |||| ||||| ||||||||||||||||| |  || ||||||||||  || || |  || ||   ||||| |   
----------------------------------------------------------------------gtagcctttttgtaaactgttggatcggcaatctttgtggttccttggatgtttaagcagtctgccatggttttgtagGCTTCACAGGATCTGTCTTCGCTCAAGGACATAGCAGGGGAGACTGGAAAGAAGCTGACATCTCTGGCCTCCAATTTCATCAGCGACCTGGACAGGATCC--

upper sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 6
------------------------------gtattctttaccttt--tactggatttggga---atttcattattcatgtcatttgtcatctgaacaacaaaatgataattga--attagtgacatt---agtttctgtattcatgttggatgg-gttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA---
                              | | | ||  | | |   ||   | || | |    ||| |     ||  | |  | | |  | | |   ||  || |||   |  |  | |  |||    ||     || |  | |||| ||   ||       | | |  |    |   || ||| ||||   ||||||||| ||||| || ||| |||| || |||||||||||||||||||| |  ||  | |||||||  || || |  || ||   |||| |||   
gtaacttgttggcataacctgttgtttcttggaattttagcgtgtagcaccatagtttgcatacgttttaagccacaattgaactatgagtt-agcggaaacgtgctaaggaaaaaccaataccatgcagagacgtcgtgtgaaagttgcataaagtcaacagtctcatttcctgtcatggttttgtagGCGTCACAGGATCTGTCTTCACTCAAGGACATAGCTGGAGAGACTGGAAAGAAGCTGACATCTTTCGCCTCCAATTTCATCAGCGACCT---GGACAGAATCC

upper sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------gtattctttaccttttactggatttgggaatttcattattcatgtcatttgtcatctgaacaacaaaatg-ataattgaattagtgacattagtttct---gtattcatgttggatgggttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA
                                         |||      ||| |  | || | |   |     | || |  |  ||  ||| ||| | |   ||||   |  || |  || |    ||   || |   | || ||      |||| ||| | |         ||  ||||   |  |||||||| || |||  |||||| || ||||  |||||||| ||||| || ||||| |||||||| ||||| || || || |||||||||||||| ||| |||
gtaactttgcagatttatgatgtttccggtttatgattaagttcgaagattttcaaagaatgttgtgctaatgatgtttagttttttcatcacctggaaatttaaatttgtgttttatgtaatttttttttcttgtcatgaatgcactacatatggattgatattgctgatgatcttctct---tcacagGCACAGCAAGATTACTCTTCTCTCAAGAGTATTGCAGGTGAGACCGGGAAGAAACTCAGCTCCCTGGCATCAACTTTAATGACAGATCTTCAAGACAGAA

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|208288972|gb|GE088009.1|GE088009
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAG
EST: gi|10255901|gb|BE823667.1|BE823667
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|254314431|gb|GR832016.1|GR832016
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|9564183|gb|BE473692.1|BE473692
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|13252312|gb|BG363215.1|BG363215
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|22524240|gb|BU083051.1|BU083051
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|254330187|gb|GR839740.1|GR839740
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|31466806|gb|CD408834.1|CD408834
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|11275201|gb|BF325524.1|BF325524
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|254338283|gb|GR849808.1|GR849808
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|7590561|gb|AW706311.1|AW706311
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTNCCTTAAGAACATTGCAGGAGAGACTGGAGAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
EST: gi|31474882|gb|CD416910.1|CD416910
EST:     ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAG                         GCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG
genomic: ACAACATCGATCTTACTGCTGGTGACCTCATCAATCGATTATCTTTCCAGgtattcttta ... tgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtattcatgttggatgggttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA
                         ctgtacgcctccctcc  CT-rich tract
     tattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctttaccttttactggatttgggaatttcattattcatgtcatttgtcatctgaacaacaaaatgataattgaattagtgacattagtttctgtattcatgttggatgggttgctgtacgcctccctcccctctgtgttgcagGCACAACAGGATCTCTCTTCCCTTAAGAACATTGCAGGAGAGACTGGAAAGAAGCTCAGCTCACTGGCCTCCACATTGATGACAGATCTTCAGGACCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA