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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcagatttctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG

Basic information

species Zea mays
transcript GRMZM2G113202_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 2
gtaagttgca-gatttctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
|||||   |   ||||  ||    ||  | ||  |   |  |  | |  || ||||| || |||  | ||  | ||   ||| ||||||||||| |||||||| ||| | ||  || |||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| ||||| |
gtaagcaacctaatttgctttgttgaaggccttatggttggtttcag--agtatgataatctgattctcagtcatctgattt-aagGTACTGAGGTTGAAAACAGAGAGCCTTGAAGCTGCAAATCCTGAAATTCTTGACGGGGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAGCCATCCG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 3
-----gtaagttgcagatttctttctaagatagtctgttctataatc-actggaagcatgatcatttgacccccacccttccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
      ||| || || || | | || |   | ||   || |    |  |||          ||      | |||      || | ||  ||||  ||| | |||||   ||  || ||  ||| ||||||||||| || ||||||||||||||||| || ||||| || |||||| ||| ||| || ||||
gtaagataaattaca-atatttctcaagagtggtgcatttttggctttactaactatgcagtctcccctctccctgtgggccttattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGAGTGGATGACCTCATGCAACTTAGTTATTTAAATGAGCCGTCAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 2
gtaagtt--gcagatttctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttcccttttta-agGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
||||| |  |  | | | ||||| |   ||  |||||  |  || ||    |  |||| |   |  | |   ||  || |  | | ||||  | |   |||||   ||| || |    || || |||||||| ||||||||||| |||||||| || ||||| ||||||||| |||  ||||||||||
gtaagataagtggctatatttctca---agaatgttcagt--tctcttttggtctgattaacagtactctttccccccttaatcatagGTTTTTAAGGTGAAAGAGGAGAGTTTGGTGCCAGCTAATCCTGATATTCTTGATGGGGTGGATGACCTCATGCAACTAAGTTATTTAAACGAACCATCAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
-----gtaagttgcagatttctttctaagatagtctgttctataatca-ctggaagcatgat-catttgacccccaccctt---ccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
      ||| || || || | | ||     | ||    |  ||  |   ||  |   |  || || |    |||||||  |   ||   ||  ||||  ||| | |||||   ||  || ||  ||| ||||||||||| || |||||||| |||||||| || ||||| || |||||| ||| |||||| ||||
gtgagataaattaca-atatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 3
-----gtaagttgcagatttctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttcccttttta-agGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
      ||||| |||   ||  |      ||  || ||||| |  |     ||   |   | | |   |||||||||   | |  | | ||||  | |   |||||   ||| || |    || || |||||||| |||||||||||||||||||| || ||||| ||||||||| ||| ||| ||||| |
gtaagataagtggcaatatttctcaagtaatgttcagttcttttttggtctgattaactgt-actcttcccccaccccctcttaatcatagGTTTTAAAGGTGAAAGAGGAGAGTTTGGTGCCAGCTAATCCTGATATTCTTGATGGAGTGGATGACCTCATGCAACTAAGTTATTTAAATGAGCCATCGG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttgcagatt-tctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttcccttttta-agGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
||||||  |   || | |||||||| ||| | | |   ||||   || ||| ||  | || |||  |          |||   | ||||  | | | | | | | |||  ||||  ||||||||||||||| ||||||||||||||||| |||||||||||||| |||||  ||| ||| |||||||
gtaagtaactttttgtatttctaaggtagccaggt---taatttttg-aagtatt-tgatctgaaactactttcaaacttgaaacagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG

upper sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttgcagattt---ctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttccctt--tttaa--gGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
||||||       ||    |  ||  |  | | |   |||   | | || |||  |  | ||  ||  |   | |||| |||  || ||  |||  | | | | ||| | |||  | ||  ||||||||||||||| |||||||||||||| || ||||| ||||| ||||||||| ||| ||| ||| |||
gtaagtgattttgttaaattccctgggtgaatgtaaacta---ttattgtaagtgtt-tgatcggaaactatctcttcacttgattcaacagGTTTTAAAAGTCAAATCAGAGACTTTAGTACCTGCAAATCCTGATATTCTTGATGGAGTAGACGATCTCATGCAACTAAGTTATTTAAATGAGCCAGCAG

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|20811148|gb|BQ295626.1|BQ295626
EST:     GTAAAGGTTTCTGAAGGGAAG                         GTACTGAGATTGAAAACCGAGTGTCTACAACCTGTCAAATCCTGAAATTCT
genomic: GTAAAGGTTTCTGAAGGGAAGgtaagttgca ... cctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTG-CAAATCCTGAAATTCT




















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: 495

GCATAGAGTTTTTTGTCAGCTTCCGAATGGCGATTGGGCATTATGCACAGTAATTACAACCTCTGGTGATGAGTCGGTTGTAAAGGTTTCTGAAGGGAAGgtaagttgca ... cctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 320

GCATAGAGTTTTTTGTCAGCTTCCGAATGGCGATTGGGCATTATGCACAGTAATTACAACCTCTGGTGATGAGTCGGTTGTAAAGGTTTCTGAAGGGAAGgtaagttgca ... cctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 374

GCATAGAGTTTTTTGTCAGCTTCCGAATGGCGATTGGGCATTATGCACAGTAATTACAACCTCTGGTGATGAGTCGGTTGTAAAGGTTTCTGAAGGGAAGgtaagttgca ... cctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 458

GCATAGAGTTTTTTGTCAGCTTCCGAATGGCGATTGGGCATTATGCACAGTAATTACAACCTCTGGTGATGAGTCGGTTGTAAAGGTTTCTGAAGGGAAGgtaagttgca ... cctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctataatcactggaagcatgatcatttgacccccacccttccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
                           atttgac  putative branch site (score: 458)
                         tcatttgacccccacc  CT-rich tract
                                               tttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgcagatttctttctaagatagtctgttctataatcactggaagcatgatcatttgacccccacccttccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT