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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcagcagtttcgagtagtcatggtgcattggtgcccgacaaggtatggcgactaactgaattgcttttattgcag

Basic information

species Zea mays
transcript GRMZM2G005036_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T02 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os05g44916.2 (Oryza sativa), 5'ss of exon 11
TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcagcagtttcgagt--agtcatggtgcattggtgcccgacaaggtatgg----cgactaactgaattgcttttattgcag
|| ||||||||||| ||||||||||||||||| ||||||||||  ||||| |||||| |||| || ||| | || || ||| ||||||| ||||| || |||||||  |  | ||   |||  |  |||||  |  ||    |    |  || ||      |||||| ||||  |||  | ||||||
TACTTCCTGAAAACTGTTGAGGAGATCACTTTAAATGACATTTCTTCAACTGCAAAGAAGATTATTTCTTCGCCGCTTACATTGGCATCATGGGGTGATGgtatgtcgaa-acttggaagttaaagcatggccctatgcaagctctgagagtctgagcactgactaattgaaacgctcgtgttgcag
















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|40333865|gb|CK367935.1|CK367935
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTT
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTT
EST: gi|89758987|gb|DY687957.1|DY687957
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
EST: gi|30031571|gb|CB833422.1|CB833422
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
EST: gi|166579063|gb|EG133278.1|EG133278
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATC-TGGGGCGACG                         TTATTCATGTTCCTAGC
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGC
EST: gi|71438038|gb|DR819088.1|DR819088
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCCAAGT
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
EST: gi|32863948|gb|CF003630.1|CF003630
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
EST: gi|211146232|gb|FL303723.1|FL303723
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTC
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTC
EST: gi|40336960|gb|CK371030.1|CK371030
EST:     CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACG                         TTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT
genomic: CGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGT

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), 48 (downstream exon)
Score: 243

TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGTGAGAGGATCCAGCATCGGACTTGCATGACCTGTTCCAACAACTGATGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 242

TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGTGAGAGGATCCAGCATCGGACTTGCATGACCTGTTCCAACAACTGATGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 137

TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGTGAGAGGATCCAGCATCGGACTTGCATGACCTGTTCCAACAACTGATGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 375

TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcag ... tttattgcagTTATTCATGTTCCTAGCTACGAGTCTGTTAGCCGCAAGTTTCACTCGAAGTGAGAGGATCCAGCATCGGACTTGCATGACCTGTTCCAACAACTGATGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTCCTGAAAACAGTTGAGGAGATCACTTTGAATGACATTTTGTCAACCGCAAAGGAGATGATGTCTACACCACTCACAATGGCATCGTGGGGCGACGgtatgttcagcagtttcgagtagtcatggtgcattggtgcccgacaaggtatggcgactaactgaattgcttttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG