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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactgcag

Basic information

species Zea mays
transcript GRMZM2G073774_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 12
GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgtttgctacttcacgtt-catgttttctccagaatttacacat------gttcttt------gtcaagttttcattaacagaatttgacaa-tatgtggtcct-cactgcag------------------------------------------------------
 || || |||||||||||||||||| ||| |||||| ||||| |||||||||||||| || ||||| |||||||||||||||||||||||  ||||||||||     |||||  || ||   |   | | |||    |||  |||   | |      ||| |||      ||   ||| || |      || ||| ||  |  ||  | ||    ||||                                                       
AAAAGCTGATAAAGAAGGATTTGAGATAAGTGTTGTTAAGACCAGCTTTAAGGCTAATACAAAAGCATTGGCAGAAAATGAAGGAGATGGACTTGCTAAGgtatacatgttt-ttagtttgtgccacttatttctatcagttttttttccttgcagggttatttctatcagttgtgttgtcttgtctccaaattggcacctgggtattgctgtcttgcatggcttcattcagtgacatactttgggcttgacaattgtatgttcctttctgcag

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 5'ss of exon 5
GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactgcag
 || || || || || |||||||| |||| |||||  |||||||| |||||||||||||| || ||  | || ||||||||||| |  ||| ||||||||||   | | |   || |||    | ||  | |  ||     |  |     |||  || |    ||||   | || | | | |    || || ||  || |     
AAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCCAAGACTAGTTTTAAGGCTAACACAAAGGCCCTAGCCGAAAATGAAGGGGCGGGGCTTGCTAAGgtgtatatata-actccttttattccagttctattctctggtacatgatggtttcttctttttttttttgttactggaataggtggtaagtagttttctcg----

upper sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 12
GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactgcag
||| || || || || |||||||| |||| |||||  ||||| ||||||||||||||||| || ||  | ||||||||||||||||| ||  |||||||||| ||  |  ||    |||| | | ||    ||||        | | |||  |||   |   ||  | ||| |     ||| |  | ||||  ||   | ||   
GAAAGCTGAAAAGGAGGGATTTGAAGTAAGTGTTGCAAAGACAAGCTTTAAGGCTAACACAAAGGCCCTAGCAGAAAATGAAGGAGAGGGACTTGCTAAGgtaatatttcttaacccttctcttccaacacttctgtgttgactccgcataatctgaat--ggtaataattgattttcttt-atgagatgttatctgaaatgt--

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|32944152|gb|CF048971.1|CF048971
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|67029833|gb|CO458582.1|CO458582
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|211287326|gb|FL348627.1|FL348627
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|13315813|gb|BG410365.1|BG410365
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|24767210|gb|CA402354.1|CA402354
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|16378693|gb|BI992557.1|BI992557
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|31362407|gb|CD446764.1|CD446764
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|78075765|gb|DV504199.1|DV504199
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|211284887|gb|FL322128.1|FL322128
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|4885872|gb|AI676992.1|AI676992
EST:     AGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|60340265|gb|DN207238.1|DN207238
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|67018763|gb|CO447512.1|CO447512
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
EST: gi|31353176|gb|CD437533.1|CD437533
EST:     AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAG                         TTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT
genomic: AGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGT

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: 48 (upstream exon), 49 (downstream exon)
Score: 158

GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 140

GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 159

GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 276

GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgt ... ctcactgcagTTGATTTACCGACCTGACACGGGTGAAATTCTTGGGGTTCACATTTTGGGTTTGCATGCTGCTGATCTCATTCACGAGGCATCAAATGCCATCGCCCTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGCAGATAAAGAAGGATTTGAGGTAAATGTTGTGAAGACTAGCTTTAAGGCTAACACTAAAGCTTTGGCAGAAAATGAAGGAGATGGGATTGCTAAGgtcattctgtttgctacttcacgttcatgttttctccagaatttacacatgttctttgtcaagttttcattaacagaatttgacaatatgtggtcctcactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG