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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccacctgataccctttatgaaactttagtatttctcaacaaatattaagatattctctttataagttaaaaaaagttagaaatcctgcaagcttaacatatgcgcttccgtcatttttccccttttggcttcatatttcaattgtgacctgaaaattctccgtgcttctacaatttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG

Basic information

species Zea mays
transcript GRMZM2G093359_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 3'ss of exon 7
gtaagccacctgataccctttatgaaactttagtatttctcaacaaatattaagatattctctttataagttaaaaaaagttagaaatcctgcaa--gcttaacatatgcgcttccgtcatttttcccct----tttggcttcatatttcaattgtgacctgaaaattctccgtgcttctacaatttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG
                                                                                         |  |||   ||| |  |     ||||| | ||||   |  |    | ||  || || ||||     ||   | | |  | ||| | || ||      | | ||||||||||  ||||||| ||||| |||||| | |||||  | ||||||||||  ||||| ||||||||||||
-----------------------------------------------------------------------------------------cgacaattacttga-gtggattcttccatgatttccgcaatggactatgcttttatctttcgtcaatg---taacatgtttccttcctactttgtgatttttagGTACCACAGTATCACCCTGGATCGTTACTATGGATGCCCTAAAGCCTTTCACCTGTGAAGCTCCTAAGCAG
















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|60358486|gb|DN225459.1|DN225459
EST:     CTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: CTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|32937713|gb|CF042532.1|CF042532
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|60401451|gb|DN234258.1|DN234258
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|60338752|gb|DN205725.1|DN205725
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|60358733|gb|DN225706.1|DN225706
EST:     TTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|12046552|gb|BF728691.1|BF728691
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGGTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|19058676|gb|BM737343.1|BM737343
EST:     TCAGGCTTGGGAGACTATACCTCTNGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|211126137|gb|FL125779.1|FL125779
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|94474487|gb|EB703445.1|EB703445
EST:     GGCTTAGGAGACTATACCTCTTGGCCCTTTCCTTGGGAAAAGCTTCA                         GTCCCCCCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: GGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|87154062|gb|DY398851.1|DY398851
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|71424524|gb|DR806343.1|DR806343
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|60397238|gb|DN230054.1|DN230054
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|149106512|gb|EE188404.2|EE188404
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
EST: gi|149106513|gb|EE188405.2|EE188405
EST:     CAGGCTTGGGAGACTATACCTCTTGGACCTTTCCCTTGG-AAAAGCTTCA                         GTACCACCATATCACCCATGGATTGTTTACTCTTGATGCTT
genomic: CAGGCTTGGGAGACTATACCTCTTGGACCTTTCC-TTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACC-ATGGATTGTT-ACTCTTGATGCTT
EST: gi|86466217|gb|DY232590.1|DY232590
EST:     TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCA                         GTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA
genomic: TCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCA

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), 45 (downstream exon)
Score: 152

CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 209

CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 163

CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 308

CCAGAGATATTCAGGCTTGGGAGACTATACCTCTTGGACCTTTCCTTGGGAAAAGCTTCAgtaagccacc ... atttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcatatttcaattgtgacctgaaaattctccgtgcttctacaatttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG
                                              tttctct  CT-rich tract
     atatttcaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccacctgataccctttatgaaactttagtatttctcaacaaatattaagatattctctttataagttaaaaaaagttagaaatcctgcaagcttaacatatgcgcttccgtcatttttccccttttggcttcatatttcaattgtgacctgaaaattctccgtgcttctacaatttctctagGTACCACCATATCACCATGGATTGTTACTCTTGATGCTTTGAAGCCTTTCATGTGTGAGGCTCCTAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC