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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaaattgttaaattttttgtttccatttatttattcttccttggacaggttggatgtattaataggttcccatagttacaagcttctattttt...

Basic information

species Zea mays
transcript GRMZM2G075153_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075153_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 5'ss of exon 7
GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaaattgttaaattttttgtttccatttatttattcttccttggacaggttggatgtattaataggt--tcccatagttacaagcttctattttt---
||||||||||| ||| ||||||||||||||||| ||||||||||||| || || || |||||||||||||||||||||||||| |||||||||||    || |||| | | | | ||      |||    |  || |     ||   |    ||  |||||  | |  || ||| || | || ||| |    
GTTATTGGAGGCTGCATCAGTGGCAGAGATGAGCTAGTTTCCAAAGTCCGCATCTATCACCATGTAGTTGGTGGTGTTCTAAATCCGgtgagtttgggctggtaaaatatctctctc-----gtttgcattgactagaggtagtgatagcccttgttaggtaattctgtaattaaaatcgtcaattgtacag
















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|89248894|gb|DY620680.1|DY620680
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|67012102|gb|CO440851.1|CO440851
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|60395696|gb|DN228566.1|DN228566
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|47962545|gb|CN845254.1|CN845254
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|78122335|gb|DV540719.1|DV540719
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|67012003|gb|CO440752.1|CO440752
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|60398293|gb|DN231109.1|DN231109
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|4647443|gb|AI622518.1|AI622518
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|76291941|gb|DV031509.1|DV031509
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|60352254|gb|DN219227.1|DN219227
EST:     CCACCATGTAGTAGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGGGGTAAGAAGACACTGCATCTCCGTGTG
genomic: CCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|71763831|gb|DR961768.1|DR961768
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|60397682|gb|DN230498.1|DN230498
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|213192843|gb|FM182914.1|FM182914
EST:     TTTCC-AAGTTCGTATTTACCACCATGTAGTTGGNNGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|149094738|gb|EE180294.2|EE180294
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|71419167|gb|DR804675.1|DR804675
EST:     TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: TTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
EST: gi|30705989|gb|CD058994.1|CD058994
EST:     CATGTAGTTGGTGGTGTTCTAAACCCG                         AATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG
genomic: CATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTG

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: 358

GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 555

GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 894

GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 441

GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaa ... gtgatattagAATGCTGCGTACCTTATCCTTCGAGGTATGAAGACACTGCATCTCCGTGTGCAATGTCAGAACGACACTGCTCTTCGGATGGCCCAGTTTTTAGAGGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGGAGGATGCGTCAGTGGCAGAGATGAGTTAGTTTCCAAAGTTCGTATTTACCACCATGTAGTTGGTGGTGTTCTAAACCCGgtgagtttaaattgttaaattttttgtttccatttatttattcttccttggacaggttggatgtattaataggttcccatagttacaagcttctattttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG