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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctttaattattcccagtgaacactcttttttttaaaatcatttttggtgataagtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT

Basic information

species Zea mays
transcript GRMZM2G011893_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011893_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g01410.1 (Oryza sativa), 3'ss of exon 10
gtgagctttaattattcccagtgaacactcttttttt--taaaatcatttttggtgataagtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT
||||||||| |  ||||  |        | |  |  |  | ||  ||| |  |||  |   ||  | || |             ||   |  | | ||   |      ||||||||||| || ||| ||||||||||| | ||||| || ||||||||| | |||||||| |||  ||||||||||||||| ||||| || || || || |||||
gtgagcttttagcattctaatgcgctggtttcatcctagtgaagccatctaaggttcttc-tgatcatggggcag---------tggctaatcctattcaatg----gcttgcagTGACCGGAAAATTGTGGCCAAAGATCTATGAAATTAAGCTACGGCCTGTAGATGGGCCACAAGATGGATCTGTAGAGAAGCTATGCCCCAAGGCAAGCTT

upper sequence: GRMZM2G011893_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G24450.1 (Glycine max), 3'ss of exon 10
----gtgagctttaattattcccagtgaacactcttttttttaaaatcatttttggtgataagtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGC---AGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT
     | ||| | ||| |     ||||||   |  | |||||    |   | ||  |   |       |  | || |||  | |  | |||   | |      |    | ||||||||||| || ||||||||||||||||| ||||| |||||| |     || || | |  |||     ||| ||  |  | ||  | |||||       |  |||  
cctaataagcatcaataa-----agtgaaagataatgtttttgctttttctcttttttcca-----tttacaactcaaa--taagtttatggaacat-----atgtcttgcttgcagTGACCGGAAAACTGTGGCCAAAGCTGTATGAAATCAAGGTTTCACCAATAAAGGAACCAATTGAAGAAGGGACCATTGAGCAACTTTGCTTGCCTG--AGCC-

upper sequence: GRMZM2G011893_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G29760.1 (Glycine max), 3'ss of exon 10
----gtgagctttaattattcccagtgaacactcttttttttaaaatcatttttggtgataagtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGC---AGATGGATCTGTAGAAAAGCTTTGTCCAAA-AGCCAGCTT
      |  |||   || | |||  |     || ||   ||| |||| | |||  |  | |  ||   ||  ||| ||   |||||  |  |   | |||||        ||| ||||||| || |||||||||||| |||||||||| |||||| |     | ||| |    |||     ||| ||     | || ||||||||       ||||     
gttaacgttcttgctttgtccccttt---tccttttacatttcaaataagtttatgcaacatatg---ttttgcttaa---tgatcaaaaaaatatgttttg--------ctttcagTGACTGGAAAACTGTGGCCAGAGCTATATGAAATCAAGGTTTCTCCTGTAAACAAACCAATTGAAGAAGGGATCATTGAGAAGCTTTGCTTGCGTAGCCC----

upper sequence: GRMZM2G011893_T02 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G24430.1 (Glycine max), 3'ss of exon 7
gtgagctttaattattcccagtgaacactcttttttttaaaatcatttttggtgataagtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGC---AGATGGATCTGTAGAAAAGCTTTGTC--CAAAAGCCAGCTT
         |||  || ||    |       ||| ||||  || |  ||| |   ||||   |  | |     || |  |     |     |    |  |    | ||| ||||||| || ||||||||||||||||| ||||| |||||| |     ||||| |    |||     ||| ||     | ||  ||||||||   |  || ||     
-----aaaaaatagtttcctaaaa-------tttatttaggattacattttgctttaagaatcaattattaacaactcaaataagttgatgtaacata-tgttttgctttcagTGACTGGAAAACTGTGGCCAAAGCTGTATGAAATCAAGGTTTCTCCAGTAAACAAACCAATTGAAGAAGGGATCATTGAGCAGCTTTGTTTGCGTAACCC-----

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|13388729|gb|BG462371.1|BG462371
EST:     GGGATAGCTTGGGATGAAAGAAGGCCCAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: GGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|60352045|gb|DN219018.1|DN219018
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|211368558|gb|FL386260.1|FL386260
EST:     TCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|78179760|gb|DV550133.1|DV550133
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|60393994|gb|DN226864.1|DN226864
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|211290372|gb|FL395524.1|FL395524
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCRGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|60348982|gb|DN215955.1|DN215955
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|8577165|gb|BE129802.1|BE129802
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|78122303|gb|DV540687.1|DV540687
EST:     TGACGTTTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|60352117|gb|DN219090.1|DN219090
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|71428221|gb|DR809271.1|DR809271
EST:     TGACGTTTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|60350066|gb|DN217039.1|DN217039
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|12047218|gb|BF729357.1|BF729357
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|60357511|gb|DN224484.1|DN224484
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
EST: gi|211246375|gb|FL451973.1|FL451973
EST:     TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTG                         TGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG
genomic: TGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAG

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: 96

AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

AATATTGACGTCTTAAACGGGATAGCTTGGGATGAAAGAAGGCACAGATTATTTGgtgagcttta ... gtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT
                     atctgat  putative branch site (score: 89)
              aaatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctttaattattcccagtgaacactcttttttttaaaatcatttttggtgataagtggccttgagctgaaatttgatctgatgagccttttttggtacggtacttgcagTGACAGGGAAACTGTGGCCAAAGCTATATGAGATCAAGCTACGGGCAGTAGATGGTCCAGCAGATGGATCTGTAGAAAAGCTTTGTCCAAAAGCCAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA