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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacccattctcttgaaatgtttttatctacttgattagagtttgtgttcctaatcctgaatcatggcagactattgcaatgatacctctcttgc...

Basic information

species Zea mays
transcript GRMZM5G887631_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g38760.1 (Oryza sativa), 5'ss of exon 7
GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacccattctc--ttgaaatgtttttatctacttgattagagtttgtgttcctaatcctga-atcatggcagac-tattgcaatgatacctctct-tgc
  ||||||||||| ||||||||||||||||||||||| ||||||||||| ||| |||||||||||||||| ||||| ||||| | ||||||||| ||||||| |||    | |  ||  |||  ||||||| ||| |||  |||| |   | ||  | ||||  |||     || ||||   |||  | | | |  | ||| || 
ACGTTGTTATGCCACCACTGCTTCAGTCTGCTCAACTGAAGCCTGATGTCACAATTACTTCAGCTGAATCTGATGATGATATAGAATCAGATGATGATAGgtttgtgcatcttcttcaattgctatgtttt-atccactgaattaaa---tatgcccttaatattgatgctgtgtcagaggcattctatttaaatttatctatg-

upper sequence: GRMZM5G887631_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA05G28950.2 (Glycine max), 5'ss of exon 9
GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCA---TCAGATGACGATAGgtctgttacccattctcttgaaatgtttttatctacttgattagagtttgtgttcctaatcctgaat-catggcagactattgcaatgatacctctcttgc--------
   |||| ||||||||||||||||| ||||||  ||| ||||||||||| ||  |||| ||||| || |||||  | || |||| |   || |||||||| ||||||       | || ||       ||| ||  ||    |||  |       | || |||  ||||| |||     |    |   || | || |||| |          
---TTGTCATGCCTCCACTGCTTCAATCTGCTTCACTTAAGCCTGATGTAACCATTACATCAGCAGATTCAGACAATGAGATTGAAGATTCTGATGACGAAAGgtctcaactttaatccct-------tttctacgtaaaaaatttaaa--caattaccaaattatgaatgcataatgtatcgcttttatcacacatctcgtcattttggtc
















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|32937524|gb|CF042343.1|CF042343
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|32937521|gb|CF042340.1|CF042340
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|71770782|gb|DR968719.1|DR968719
EST:     ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|32935366|gb|CF040178.1|CF040178
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|32935549|gb|CF040361.1|CF040361
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|32850147|gb|CD989828.1|CD989828
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|32937789|gb|CF042608.1|CF042608
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
EST: gi|32850586|gb|CD990267.1|CD990267
EST:     ACAGTTACTTCAGCCGAATCAGATGACGATATTGCATCAGATGACGATAG                         CATTGAAACAATCACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT
genomic: ACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGT

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: 326

GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGTGCTGGAAGAGAAAGCAACAGCTTGCAACATGCTGTGCTGTTATGCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGTGCTGGAAGAGAAAGCAACAGCTTGCAACATGCTGTGCTGTTATGCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 513

GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGTGCTGGAAGAGAAAGCAACAGCTTGCAACATGCTGTGCTGTTATGCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 240

GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacc ... ttctatacagCATTGAAACAATTACACTTGGTGACAAAAGAATAGGAATTCGAACTAGTGTGCTGGAAGAGAAAGCAACAGCTTGCAACATGCTGTGCTGTTATGCTGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTGTTATGCCTCCACTGCTTCAGTCTGCTCAACTCAAGCCTGATGTTACAGTTACTTCAGCTGAATCAGATGACGATATTGCATCAGATGACGATAGgtctgttacccattctcttgaaatgtttttatctacttgattagagtttgtgttcctaatcctgaatcatggcagactattgcaatgatacctctcttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG