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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtatttttttatccacatactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT

Basic information

species Zea mays
transcript GRMZM2G472625_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 6
gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtatttttttatcca-catactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
   | || | ||| |  ||   | |      ||| |   ||| || |    | |  | ||||| | |  | | | || |  ||| | |  | ||    ||| |||||||||||||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||| || || ||||||||||||||||| |||||||
-cttggattataactgttggcctctcttccctagttctgttatttcttcattttgctattttaacaaatagattgatgatctccttgtactattccaccagGTTCCTGGTGAACCGAACATATCATACATTTGCTCTCGCTATTATCGTGCTCCTGAGCTCATATTTGGTGCAACCGAGTATACAACTTCAATTGACATAT

upper sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 6
gaattgactgtaattcatgtgtt-ataacaattagattctttacttgtatgctgtatttttttatccacatactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
 |  | ||  ||    ||   || ||  || || |   |  | | | | | | |      | | | |   | ||||  |  | || || |||| |  |||| |    |||||| | || ||||| |||||||| || || |  |||||||||||||| || |||||||| || || |||||||||| |||||| || || |
catcttacaatatccaataaattgatttcactttgtgcccctccctcttttccggcagaatgt-ttcttgttctaacaaccttcaaattttgtctcatcagGTAAAAGGTGAAGCTAATATATCATACATATGTTCACGATTCTATCGTGCTCCAGAACTTATATTTGGTGCCACAGAGTATACAAGTTCAATTGATATTT

upper sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtat-ttttttatccacata---ctaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
                                                                       | || |||| |  |    | | |     | |     | |||  ||   || | || || | | |     ||   ||  | | ||     |  |    | | || |    |||||||| |||||||| || || ||||| |||||||||||||||||||| || || ||||| || || ||||||||| | || ||||| ||||
gtaagggtgttatcttttcattatctcaccttttttgtgtgttttcggcttggttatgtatctacgcatctagttcactg-agctaccatataagtgtgagttataccattaagtgcgagcagcatgttctctgttttggtaacccttttaaatttttggtaattcactattagGTCAAAGGTGAACCAAACATATCATATATCTGCTCCCGTTATTATCGTGCTCCAGAACTGATCTTTGGCGCCACAGAGTATACAGCATCCATAGATATAT

upper sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 6
gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtattttt----ttatccacatactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
   || |  ||| |   |      ||  ||  | | ||||| ||||| |  | | | | |    |  | ||  |  | | ||  |  ||    | |||  |||| ||   |||||| | |||||||| |||||||| |||||||  || || || || || ||||||||||| || || ||||||||||| ||||| || ||||
tctttcatggtagtcagtactcagtaggaag-aaagtctttgcttgttttttctttctatgatatctttcatgttttcacca--tgaatccaat-tttcatcagGTTAAAGGTGAAGCAAACATATCATACATATGTTCTCGTTTCTACCGAGCACCTGAACTCATATTTGGGGCCACAGAGTATACAACCTCAATTGATATAT

upper sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 5
gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtatttttttatccacatactaatcagttccatatgttg--ttttgt-cagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
 | | |   ||||  ||  ||  || |  | |   ||||   ||     | || || |||   |  | | | |    |     | |  | |  |  ||| ||| |    || ||||| ||||| || || || || || || ||||| |||||||| ||||| ||||||||||||||||| || || ||| | ||||||||||
-agtagtgggtaa--cacatggcatgaataatgtcttctccgctatcgagttgaatatttgagtggagaaagtggcgacactgagaattcgagtactgtgcagGTGAAAGGGGAACCTAACATCTCGTATATCTGTTCACGGTATTACCGTGCTCCTGAGCTGATATTTGGAGCGACGGAATACACCACTGCGATAGACATAT

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|33095534|gb|CF055528.1|CF055528
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|18660957|gb|BM501137.1|BM501137
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|6695759|gb|AW288837.1|AW288837
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|13198123|gb|BG354164.1|BG354164
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACAT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACAT
EST: gi|6587591|gb|AW244909.1|AW244909
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         ATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGNTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
EST: gi|9825069|gb|BE575271.1|BE575271
EST:     CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG                         GTTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT
genomic: CTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCT

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), 47 (downstream exon)
Score: 424

GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 157

GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTGgtatgttgtt ... gttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgctgtatttttttatccacatactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT
                        tactaat  putative branch site (score: 157)
                                           ttgtttt  putative PPT
      tgtatttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattgactgtaattcatgtgttataacaattagattctttacttgtatgctgtatttttttatccacatactaatcagttccatatgttgttttgtcagATTCCTGGTGAACCGAACATATCTTACATATGCTCTCGTTATTATCGTGCTCCAGAGCTCATATTTGGAGCGACGGAGTATACAACTTCAATAGACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG