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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcattgttggaaaaattgccttc...

Basic information

species Zea mays
transcript GRMZM2G158021_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g43470.1 (Oryza sativa), 5'ss of exon 5
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatct---ccaaaagtttcttgacaccattttcttctttgaaattg-acatgatttcaacaaaaaaaaacttttgcattgttggaaaaattgccttc-
||| ||||||| ||||| ||||| || |||||||||||||||||||| |||||||| |||||| |     ||   |  | |||||         | |       ||| | ||| | ||  |||          |||| ||||  ||  ||     | |  |||  
CTTTTAGATCTTCCAGGAATCATTGAGGGTGCTAAAGATGGAAAGGGTAGAGGAAGGCAGgtaatatgtcctgctctcacagttttgaattggtactaatgctattggatttgtatattcttttgcactgtgtaaacatttgtttttctg-----actctctttg

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G15180.2 (Glycine max), 5'ss of exon 5
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcatt--gttggaaaaattgccttc-
 |  | |||||||| || || ||||| |||||||| ||||||||||| |||||||| ||||||    ||   |  | |||||  |  ||  ||  | ||   |  | |||| || ||||  |  || | |     ||   ||   |   |  || ||   |  
TTGTTGGATCTCCCCGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaagacc--atagtttactttcattatggt-ttaactacatttgatatcatttttaacaagatagttacttaatttcaatcaaagtaactgaagtgt

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G39690.1 (Glycine max), 5'ss of exon 5
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcattgttggaaaaat-tgccttc-
 |  | |||||||| || || ||||| |||||||| ||||||||||| |||||||| ||||||    ||   ||| | ||||  |  |  |||  | ||   |  | |||| || ||||  |  || | ||  |    ||  ||     || | |  |||  
TTGTTGGATCTCCCTGGAATTATCGAGGGTGCTAAGGATGGAAAGGGTAGAGGAAGGCAGgtaaaaaaaagaccata-gtttactttcgtcatggt-ttaactacatttgatatcatttttaagaagataatttcaatcaaagtaactgaagtgtatctttt

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 5
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtat-ttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcattgttggaaaaattgccttc
 |  ||||||| || || || || || ||||||||||||||||| || |||||||||||||||  | || |||    || | ||||||    ||||| |  |||||   |    ||||        |     |||||   |||    |             
TTATTAGATCTTCCTGGTATTATTGAGGGTGCTAAAGATGGAAAAGGTAGAGGAAGACAGgtaagtcgagtct----aaatctcttgag--tattttatattttgaccctctt-tgatcatctttca----cactttactatttccag-------------

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ34569 (Selaginella moellendorffii), 5'ss of exon 4
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcattgttggaaaaattgccttc
||||| |||||||| || |||||||||||||| ||||||||||| ||  ||||  | ||||||     |  |     ||  | |||  |  |    || ||    || || | |  |     ||                                    
CTTCTCGATCTCCCTGGTATCATCGAAGGTGCAAAAGATGGAAAAGGACGAGGTCGCCAGgtaaggtgaattttttgagaatattgctatgaagagctactc---aaatgtctttgtcctggcag-----------------------------------

upper sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ09453 (Selaginella moellendorffii), 5'ss of exon 5
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcattgttggaaaaattgccttc
||||| |||||||| || |||||||||||||| ||||||||||| ||  ||||  | ||||||     |  |     ||  | |||  |  |    ||  |    || || | |  |     ||    |  |                            
CTTCTTGATCTCCCTGGTATCATCGAAGGTGCAAAAGATGGAAAAGGACGAGGTCGCCAGgtaaggtgaattttttgagaatattgctatgaagagctattc---aaatgtctttgtcctggcaggttatcag---------------------------

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|32836870|gb|CD976548.1|CD976548
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|32837261|gb|CD976939.1|CD976939
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|71769273|gb|DR967210.1|DR967210
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|32919863|gb|CF024675.1|CF024675
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|32839263|gb|CD978944.1|CD978944
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|32848352|gb|CD988033.1|CD988033
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|67034867|gb|CO463400.1|CO463400
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|60353675|gb|DN220648.1|DN220648
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|74240038|gb|DT647952.1|DT647952
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|14203739|gb|BG837416.1|BG837416
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATKTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|71418217|gb|DR804368.1|DR804368
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|76937221|gb|DV175090.1|DV175090
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|71436936|gb|DR817986.1|DR817986
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|30306602|gb|CD001275.1|CD001275
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|32836351|gb|CD976029.1|CD976029
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|67042509|gb|CO468764.1|CO468764
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|33094247|gb|CF054241.1|CF054241
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|22542275|gb|BU092713.1|BU092713
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GGTATCAGCACAGCTAGGACATGCAATG
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATG
EST: gi|87155566|gb|DY400355.1|DY400355
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|71312952|gb|DR792998.1|DR792998
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|74233974|gb|DT641888.1|DT641888
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|60343127|gb|DN210100.1|DN210100
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|6527040|gb|AW216258.1|AW216258
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|60353517|gb|DN220490.1|DN220490
EST:     GAAAGGGCAGAGGAAGACAG                         GTTATCAGCTCAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
genomic: GAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC
EST: gi|211268507|gb|FL142966.1|FL142966
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCMGAGGAAGACAG                         GTTTATCAGCACAGCTAGGACATGC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTT-ATCAGCACAGCTAGGACATGC
EST: gi|32836350|gb|CD976028.1|CD976028
EST:     TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAG                         GTTATCAGCACAGCTAGGACATGCAATGGTATTTTGATTGCTCTTGATGCC
genomic: TCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 488

CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 678

CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 517

CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 536

CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaat ... ggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTAGATCTCCCAGGGATCATCGAAGGTGCTAAAGATGGAAAGGGCAGAGGAAGACAGgtatttgaatctccaaaagtttcttgacaccattttcttctttgaaattgacatgatttcaacaaaaaaaaacttttgcattgttggaaaaattgccttc

- - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaaat