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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaaatatttgatcctgcagccctaagtatattgacttgggaagttgggactgaagttttcattgagtgatgactgatgatcctggttatttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG

Basic information

species Zea mays
transcript AC191251.3_FGT005
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC191251.3_FGT005 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g57130.1 (Oryza sativa), 3'ss of exon 1
ttaaaatatttgatcctgcagccctaagt----atattgacttgggaagttgggactgaagttttcattgagtgatgactgatgatcctggttatttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG
  |||  | || ||    ||    |   |     |   | ||    |  |||||| |  || |||  |||  | | || |         |  |  || || ||||||||||| |  | | | |||||||||| ||| || |||||||||| ||| ||||| |||||||||||||||
-caaagaaattcataaatcattgttggtttctcgtcacgcctgaccattttgggaatagagattttgttgcctaacgattttca---tggacttctttttccagAAGCGAGAGATTTTTCAGGATCTTGCTCCACTCCTGTGGCACTCTTATGGAACAATTGCTGCACTACTCCAG

upper sequence: AC191251.3_FGT005 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G43220.1 (Glycine max), 3'ss of exon 1
ttaaaatatttgatcctgcagccctaagtatattgacttgggaagttgggactgaagttttcattgagtgatgactgatgatcctggttatttc--tttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG
  |  || || | |  |     | |    || ||   | | |  | || |  |  ||   |   | |   ||| ||      | || || |||   ||| ||||| | ||   || | |||||||||||| | | |||||| | |||||||||||||| ||||||||  | |||
-cacgat-ttggcttgttttttcttgtaaatgtttggtagtgctgatgtgcttatagaggtatctcatcaatgtctttcttccatgtttttttgcattttagAAGAGGGAGCTATTTCAAGATCTTGCTCCATTGCTATGGAATTCTTTTGGTACAATTGCTGCACTTTTGCAG
















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|71757156|gb|DR955093.1|DR955093
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|148981581|gb|EE027738.2|EE027738
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|211005972|gb|FL170680.1|FL170680
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|211005967|gb|FL170675.1|FL170675
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|50336378|gb|CO531504.1|CO531504
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|211005968|gb|FL170676.1|FL170676
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|211003194|gb|FL170674.1|FL170674
EST:     ACCTGTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|211005974|gb|FL170682.1|FL170682
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|211005971|gb|FL170679.1|FL170679
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
EST: gi|37416608|gb|CF645956.1|CF645956
EST:     ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAG                         AAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT
genomic: ACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGT

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: 46 (upstream exon), 49 (downstream exon)
Score: 40

GCATCAGGACGCGGCGAAGGAGGATCAGGACGTGGCGCAGCTCGTGCTCAACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 10

GCATCAGGACGCGGCGAAGGAGGATCAGGACGTGGCGCAGCTCGTGCTCAACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG


Block sizes: 43 (upstream exon), 41 (downstream exon)
Score: 10

GCATCAGGACGCGGCGAAGGAGGATCAGGACGTGGCGCAGCTCGTGCTCAACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 40

GCATCAGGACGCGGCGAAGGAGGATCAGGACGTGGCGCAGCTCGTGCTCAACCTCTGCATCCCGGAGCTCCGCGAGAAGGCCATCATCATCCTTTCCAAGgtgaatgacc ... tttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggactgaagttttcattgagtgatgactgatgatcctggttatttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG
                           gactgat  putative branch site (score: 40)
                                          ttatttctttc  putative PPT
                                          ttatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaaatatttgatcctgcagccctaagtatattgacttgggaagttgggactgaagttttcattgagtgatgactgatgatcctggttatttctttcagAAGCGAGAAAAATGTGAAGATCTTGCTCTACTACTATGGCACTCTTTTGGTACAATGGCTGCACTACTCCAG

- - - - - - - -ctgcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgat