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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcttaatagcctgatgttgaatgcatcacctggttcacactaaatcataataggaaagtcccttcatacatgctatatattctcttctgatgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT

Basic information

species Zea mays
transcript GRMZM2G166145_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166145_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g05680.1 (Oryza sativa), 3'ss of exon 1
agcttaatagcctgatgttgaatgcat-cacctggttcacactaaatcataataggaaagtcccttcatacatgctata--tattctcttctgatgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT
   |   |   |||    |  |||||  ||         |   | | | | | |   ||||  | |||  ||||  |||          |||  |||||||||||| |||||  | |||||||| ||||||||  || | || ||||| ||||| || |||||||||||||| || ||||| |||| |||||| |||| | ||
---tatgtcctctgcgaatctatgcagacaataaacaagcttcatacccttacacttaagtatcatcaatcatgtcataatcggctatatcttctgatgacagGAAGGACTATTTAGAGATCCCTTGGGCTGAATTGAGATCAATGGTTGAACCCTCTTTTGCTGAGAGATCATTAATCTATCACAGAGATTATCTCACCAAT
















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|211065960|gb|FK946605.1|FK946605
EST:     CTCCTCGCCAAGACTATGCAGAGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTAMCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|89764195|gb|DY691091.1|DY691091
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|17970292|gb|BM277055.1|BM277055
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCA
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCA
EST: gi|18649885|gb|BM498704.1|BM498704
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGNCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|76915403|gb|DV165969.1|DV165969
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|148978860|gb|EE026348.2|EE026348
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCCTGGTCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|86470824|gb|DY237194.1|DY237194
EST:     CTCCTCGCCAAGACTATGCGGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCGTGGTCGACCC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|76285541|gb|DV025109.1|DV025109
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
EST: gi|71431205|gb|DR812255.1|DR812255
EST:     CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCC                         GAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC
genomic: CTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACC

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: 41

CGGAGGAGAAGGCGAGGGTCGTGGTGGTTGGCGGCGGCGTCGCCGGCTCCCTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

CGGAGGAGAAGGCGAGGGTCGTGGTGGTTGGCGGCGGCGTCGCCGGCTCCCTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

CGGAGGAGAAGGCGAGGGTCGTGGTGGTTGGCGGCGGCGTCGCCGGCTCCCTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 124

CGGAGGAGAAGGCGAGGGTCGTGGTGGTTGGCGGCGGCGTCGCCGGCTCCCTCCTCGCCAAGACTATGCAGGGCCACGCCGACGTCGTCCTCCTCGACCCgtaaggcttc ... atgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcataataggaaagtcccttcatacatgctatatattctcttctgatgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT
                                        ttctgat  putative branch site (score: 124)
                             tatatattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcttaatagcctgatgttgaatgcatcacctggttcacactaaatcataataggaaagtcccttcatacatgctatatattctcttctgatgatgacagGAAAGACTACCTGGAGATCCCCTGGGCTGAGCTGCGCTCCATGGTCGAACCGTCCTTTGCTGAGAGATCGTTGATCTACCACAAAGATTACCTCAGCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - cctgatg
- - - - - - - - - tgaatgc
- - - - - - - - - - - - - -cacctgg
- - - - - - - - - - - - - - - - - - -acactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacatgc