Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataccacagcaatgttactatggctctccgtttccatactgaaatccaagatatgcctgaccatctggcactcatttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG

Basic information

species Zea mays
transcript GRMZM2G071620_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071620_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g54170.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------gtaataccacagcaatgttactatggctctccgtttccatactgaaatcca---agatatgcctgacca-tctggcactca--tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
                                   |  |||| |||  |  || | ||    |  |  ||||  |    || ||        | |  || |    ||    | | |  ||| || |||||||||||||| ||||| || |||||||| ||||||||||||
gtaacactgaaatatcttcttcaatgccgccaaatgatatactacactacagtgaatacttgtacctctttcagtggcaaattcggtttgtttttatctaattgctccaatattgaacttttcttcagGAACAAATGCTACAAGATGCAAACAGGGTCCTGAAAAGGAAG
















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|78085638|gb|DV514031.1|DV514031
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|78104752|gb|DV523170.1|DV523170
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|78104753|gb|DV523171.1|DV523171
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTANAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|211236050|gb|FL156597.1|FL156597
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|30031660|gb|CB833511.1|CB833511
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|50326015|gb|CO521141.1|CO521141
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCT
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCT
EST: gi|71448410|gb|DR829460.1|DR829460
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|18174972|gb|BM350360.1|BM350360
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTAAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|71762711|gb|DR960648.1|DR960648
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|50326014|gb|CO521140.1|CO521140
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|32165114|gb|CD670432.1|CD670432
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|50325855|gb|CO520981.1|CO520981
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGG
EST: gi|31558052|gb|CD527264.1|CD527264
EST:     TTTGCGTCTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: TTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|76285216|gb|DV024784.1|DV024784
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTANAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|32836421|gb|CD976099.1|CD976099
EST:     ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAG                         GAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
EST: gi|91878815|gb|EB408772.1|EB408772
EST:     TGCGACTTAAAGAGAAAG                         GAACAAATGGTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
genomic: TGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 92

ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG


Block sizes: 42 (upstream exon), 42 (downstream exon)
Score: 22

ACTCAGGTGTTACTTGATGAACTTTGCGACTTAAAGAGAAAGgtaataccac ... tttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttccatactgaaatccaagatatgcctgaccatctggcactcatttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG
                         gcctgac  putative branch site (score: 22)
                                         ctcatttcct  putative PPT
                  aagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataccacagcaatgttactatggctctccgtttccatactgaaatccaagatatgcctgaccatctggcactcatttcctgcagGAACAAATGCTGCAAGACGCTAACAGGGTTCTGAAAAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA