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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggcccatacacctgttcctgctaatagagcatatcgattttgctatgacttttttccctaaagttttaacatgaacaatatctatcctgttta...

Basic information

species Zea mays
transcript GRMZM2G157068_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g03410.2 (Oryza sativa), 5'ss of exon 2
AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggcccatac-acctgttcctgctaatagagcatatcgat-tttgctatg---acttttttccctaaagttttaacatgaacaatatctatcctgttta
| |||||||||||||||||||||| ||||||||| ||| ||||||||||||||||||||||||| ||||| ||||| ||||| || || |||||||||||||||||||    |||| | ||  || | |   | | ||| |  | | ||||||||    |||  || | || |  |||||     | | | |||  |  |     
AGAGAGAAGTGAAGATTCTTAAAGAACTTAAAGGCCATGAGAATATTGTTCACTTCTACAATGCGTTTGAAGATGACTCATATGTATATATTGTGATGGAgtaagtagttatatactagcttctcttacatttcgtgcacaatgttatttgctatatacactccttgcacttacattttatttctacctaaatcc-taata----

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G08180.1 (Glycine max), 5'ss of exon 3
AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggcccatacacctgttcctgctaatagagcatatcgattt--tgctatgacttttttccctaa--agttttaacatgaacaatatctatcctgttta
|  ||||||| |||||  | |||| ||||| ||| ||| | ||| | ||||| ||| | ||||| ||||| ||||| |||||||||||||| || |||||||||||             |  ||    |  || |     || || |  |  ||||| |||   |   |   |  |  ||  |   |   || |||| |     
AGCGAGAAGTCAAGATATTGAAAGAACTTACAGGCCATGAAAATGTGGTTCAGTTCCATAATGCTTTTGATGATGAATCATACGTGTACATAGTTATGGAgtaagttatttttattttttagtctcttttctatactgcttcaatgtgttaatatgattttgagcatcacttaactgcaatgtactccggatatatcttt----

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G23870.1 (Glycine max), 5'ss of exon 4
AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggcccatacacctgttcctgctaatagagcatatcgattttgctatgacttttt------tccctaaagttttaacatgaacaatatctatcctgttta--------------------
|  |||| || |||||  | ||||||||||  || ||| ||||| | ||||| ||||| ||||| ||||| |||| ||| || |||||||| || ||||||||||| |  |     |  || | ||| |    |    | | | | |   | | |  |||       ||  |      | ||    | |||  | |    ||| |                     
AGCGAGAGGTCAAGATATTGAAAGCACTTACTGGCCATGAGAATGTGGTTCAGTTCTATAATGCTTTTGAAGATGGTTCTTATGTGTACATAGTTATGGAgtaagttgctctgc-tagttgattctgttttgtgtttgtgttgctctgatttttagctttggatttatctttgggagctcaattctatcaaattttggtttgtgtgtgtatatatgtgtttcctag

upper sequence: GRMZM2G053868_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G37100.1 (Glycine max), 5'ss of exon 3
AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagt-aggcccatacacctgttcctgcta-atagagcatatcgattttgctatgacttttttccctaa--agttttaacatgaacaatatctatcctgttta
|  ||||||| |||||  | |||| ||||| ||| ||| | ||| | ||||| ||||  ||||| ||||||||||||||||| |||||||| || ||||||||||| |    |||      ||  ||  |  |||  || |     | ||  ||||  |||   |   |   |  |  ||  |   |   || |||| |     
AGCGAGAAGTCAAGATATTGAAAGAACTTACAGGCCATGAAAATGTGGTTCAGTTCTTTAATGCTTTTGAGGATGATTCATATGTGTACATAGTTATGGAgtaagttattttcattttttagtctcttttctatactgcttcaatgtgttcatatggttttgagcatcacttaactgcaatttactctggatatatcttt----

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|211195521|gb|FL100645.1|FL100645
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
EST: gi|211195523|gb|FL100647.1|FL100647
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCCAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
EST: gi|149082402|gb|EE171589.2|EE171589
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
EST: gi|211195530|gb|FL100654.1|FL100654
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGGGAACTATTAGATCGGATTTTGGGCAAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGG-CAAA
EST: gi|211195524|gb|FL100648.1|FL100648
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
EST: gi|211320124|gb|FL100655.1|FL100655
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAA
EST: gi|211195522|gb|FL100646.1|FL100646
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
EST: gi|211195528|gb|FL100652.1|FL100652
EST:     CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGA                         GCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA
genomic: CACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA

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), 42 (downstream exon)
Score: 31

AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 64

AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 123

AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 69

AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggc ... gtttttgcagGCTATGTGAGGGCGGTGAACTATTAGATCGGATTTTGGCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAGAAGTGAAGATTCTTAAAGCACTTAAAGGACATCAGAATATTGTTCACTTCTACAATGCATTTGAGGATGATTCATACGTGTACATTGTGATGGAgtaagtaggcccatacacctgttcctgctaatagagcatatcgattttgctatgacttttttccctaaagttttaacatgaacaatatctatcctgttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA