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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgtcatgtggacaaggtttcgttctttctttgatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG

Basic information

species Zea mays
transcript GRMZM2G472625_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 5
gtacgtgtcatgtggacaaggtttcgttctttctttgatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
||| |  | ||||| |||||| | | ||  |||| |   |||||   | ||| |||  ||||||     | |||    |||||||||||||||||||| || || |||||||| ||||||||||| || ||||| || |||
gtatgacttatgtgaacaaggctacattacttctcttgcttggttgtttgttttgaactggtctctaattgcttgctgatacagGTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 5
gtacgtgtcatgtggacaaggtttcgttctttctttgatt--tggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
      || |  |  |  || || |  | ||||||  |    | | |  || || |   |    ||  |     |||| | |  |||||||||  ||||| ||||| |||||||||||||| ||||| || |||||||| |||
------gtaagtt--attagtttgctatttttcttcaaggaatagcatttatttattc-taaacctattttccatttgttctgtagGTTGATCGACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
gtacgtgtcatgtggacaaggtttcgttctttcttt-gatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
         | ||    ||  |    || || ||   |   | | |  || || | | |    ||  |     |||| | |  |||||||||| ||||| ||||| |||||||||||||| ||||| || |||||||| |||
-------gtaagttattaatttgctatttttcctcaaggagttgcatttatttatta-taaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 5
gtacgtgtcatgtggacaaggtttcgttctttctttgatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
||| ||        |||        |||  ||     | |  || || | | |     ||   | ||  ||   |  | ||||||||||||| || || ||||| || ||||| ||||||||||| || |||||||| || 
gtatgttcttctctgac-------tgttgcttaaaataatgagtcacaactgcatcaatgaattaatttttggcttctctacagGTTGATCCACTTACTCACCAAGTTAAGCTTTGTGACTTTGGAAGTGCAAAAGTGCTA

upper sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtacgtgtcatgtggacaaggtttcgttctttctttgatttggtaactagttctgagttggtctgatccttctttgata--tacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
                    ||    | |||       |  | |  ||    |      |      ||  |  || |||| ||| | |||     |||  | |||||||||||||||||||| ||||| ||||| ||||| ||||| || ||||| || |||
gtatattgttcattttttgataaagattatggcatgctgaatcccctccccttcccccctttcctttaaat--gacttggactgtttctttgaacataattgcagGTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG

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:     ATAATGTGCCAGGAGTCTGCCATAGGGATGTAAAGTCACAAAACGTTTTG                         GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
genomic: ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
EST: gi|6695759|gb|AW288837.1|AW288837
EST:     ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTG                         GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
genomic: ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
EST: gi|13198123|gb|BG354164.1|BG354164
EST:     ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTG                         GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
genomic: ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
EST: gi|20811237|gb|BQ295715.1|BQ295715
EST:     ATAATGTACCCGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTG                         GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAA
genomic: ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAA
EST: gi|6587591|gb|AW244909.1|AW244909
EST:     CCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTG                         GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
genomic: CCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
EST: gi|9825069|gb|BE575271.1|BE575271
EST:     ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTG                         GTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA
genomic: ATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAA

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: 327

CTTTTCAGAGGCCTAGCCTATATTCATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 94

CTTTTCAGAGGCCTAGCCTATATTCATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

CTTTTCAGAGGCCTAGCCTATATTCATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

CTTTTCAGAGGCCTAGCCTATATTCATAATGTACCAGGAGTCTGCCATAGGGATGTAAAGCCACAAAACGTTTTGgtacgtgtca ... tgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttgatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
                                tctgatccttcttt  CT-rich tract
                                           tttgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtgtcatgtggacaaggtttcgttctttctttgatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT