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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcag

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 11
GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcag
| || || ||||||||  |||||||||||||||||||||| |||||||||||||||||||||||   |  ||||||| | ||   | |  ||  ||       |  |||||     |  |  | ||     | ||  || | |   ||| |   ||   |||  |||         | || || |  | ||  || |   ||| | |||
GCCGATTTCTTGCTGAATTGACAAAAGAAGTATTTTCTGATCTTGAAGCAAGTAAATATCAGgtacttctttctttctttaccaatctcatatttg-------tgattctttaaggtggtgttgttcgctatttgtcatgtaacacattgt--ttacatattgctctg-------tctaattattcctactctca-taatcttcaccag

upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 10
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 5'ss of exon 10
GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgt--gtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcag
|||||||| | || ||| ||||  |  |||| |||||||| ||| |||||||||||||||||||  |||  || |    | |     | || |    | |  ||| || | ||     ||   |  |             | ||    ||| |    ||| |                                                 
GTCGCTTCTTAGCAGAGTTGACTCATCAAGTTTTTTCTGATCTTAAAGCAAGTAAATATCAGgtcagtgcaataccgaaagaggccatgttgtcgtggttttaacgagctattggtgattgccacttgggattcgcatggtttttcaaattttcatcattga-------------------------------------------------
















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|71772853|gb|DR970776.1|DR970776
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATC
EST: gi|74237693|gb|DT645607.1|DT645607
EST:     GAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: GAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
EST: gi|71299098|gb|DR785546.1|DR785546
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
EST: gi|32835884|gb|CD975562.1|CD975562
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
EST: gi|32863100|gb|CF002782.1|CF002782
EST:     CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAG                         ATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC
genomic: CTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGAC

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: 238

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 303

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttatt ... cctttatcagATGGCTGAGTATCGGATATCTATTTATGGGAGGAAGAAAAGCGAATGGGACCAAATGGCAAGTTGGATAGTGAACAATGAATTATATAGCGAGAATGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGCTTCCTTGCTGAGCTGACAAAAGAAGTATTTTCTGACCTTGAAGCAAGTAAATATCAGgtgtgttattctttcataacttgttttctacgtgctggaactagttcttctgatttcttatctttctagtatgctatcttatggattctagctattcatttttctagaaaggacccaactaatgattcttgcaattgcctttatcag

- - - - - - -  AGCTGA
- - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - AAGAAG
- - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - AGCAAG