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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctacatctaccacacaaattggccaacaatagtcccttcttcgttacattctatccatagtgtttgcatttaatattatttatttataaatgat...

Basic information

species Zea mays
transcript GRMZM5G863152_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G863152_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g18720.1 (Oryza sativa), 5'ss of exon 7
GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctacatctaccacacaaattggccaacaatagtcccttcttcgttacattctatccatagtgtttgcatttaatat-tatttatttataaatgat
|||||||||||  | || ||  |  | |||||| ||||||||||||||||||||||||| || |||||||||||  || || |||      | |  | |  ||  ||  | |||| |  | ||  || |    || | |||  |  || | |  |  || || | |      
GTTGGAATTGGCATAGCTGTCATGGTCTTTGGATTAGTCTTCGCTTTTGGGGATTTCCTTCCATATGGAAGgtgt-tcaacttctgttgt-cgatgtagataattat--ttccttgt--gcta-gttttgattattg-gttaactctttacacgtccttgttcacag-----
















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|166596764|gb|EG145516.1|EG145516
EST:     TTATATTTGGACTAGTCTTCGCTTTTGGGGAATTTCCTGCCTTATGGAAG                         TGTTAGCCCTAGCAAAGAAAGTG
genomic: TTATATTTGGACTAGTCTTCGCTTTTGGGGA-TTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTG
EST: gi|166654390|gb|EG123193.1|EG123193
EST:     GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG                         TGTTAGCCCTAGCAAAGAAAGTG
genomic: GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTG
EST: gi|71305070|gb|DR788672.1|DR788672
EST:     GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG                         TGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
genomic: GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
EST: gi|76920373|gb|DV168136.1|DV168136
EST:     GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG                         TGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
genomic: GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
EST: gi|211226058|gb|FL296374.1|FL296374
EST:     TATATTTGGACTAGTCNNTCGCTTTTGGGGATTTC-TGCCCTAATGGA-G                         TGTTAGCCCTAGCAAA-AAAGTGCAGTAAGTTA
genomic: -ATATTTGGACTAGTCT-TCGCTTTTGGGGATTTCCTGCCTTA-TGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTA-GTTA
EST: gi|71432424|gb|DR813474.1|DR813474
EST:     GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG                         TGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
genomic: GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
EST: gi|78081578|gb|DV509990.1|DV509990
EST:     GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAG                         TGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA
genomic: GTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 77

GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGAGGAAGAAGAAAAATTTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 85

GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGAGGAAGAAGAAAAATTTAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 40

GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGAGGAAGAAGAAAAATTTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctac ... actttttcagTGTTAGCCCTAGCAAAGAAAGTGCAGTAGTTAAACAAAAGCTTTCTCAAGAGGAAGAAGAAAAATTTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGAATTGGTGTTGCAGTTGTTATATTTGGACTAGTCTTCGCTTTTGGGGATTTCCTGCCTTATGGAAGgtgaatctacatctaccacacaaattggccaacaatagtcccttcttcgttacattctatccatagtgtttgcatttaatattatttatttataaatgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG