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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgtattttcactcttctgcaacacttagaatttctctgtattttcactcttctgcaacacttagaatttctctcagtgcttatgttatagtattcaacctaacgttctgattgatgaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT

Basic information

species Zea mays
transcript GRMZM2G166345_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 7
gtgctgtattttcactcttctgcaacacttagaatttctctgtattttcactcttctgcaacacttagaatttctctcagtgcttatgttatagtattcaacctaacgttctgattgatgaccgac--cagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT
                                   | | |   | |||    ||| ||||||| ||  || |  | |||    || | || |  | ||  | | ||  |||| | || |  |      |||||| || |||||||||||||||||||||||||| ||||||| ||||||||||||||| ||||| ||||  | ||||||||| || |||  |
----------------------------------gtacccataacttttctgcttatgcaacaattcaaaatggt-tcaacagttgtattgtgctctttgaacaaatattctaactggtctctcttttcagCCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTT
















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|32913187|gb|CF017999.1|CF017999
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|31363989|gb|CD448344.1|CD448344
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGCAAGCATCCATCTGCTGTCAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|32863847|gb|CF003529.1|CF003529
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|149110254|gb|EE294046.2|EE294046
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|211207476|gb|FL411825.1|FL411825
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|56462002|gb|CK986300.1|CK986300
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|83279363|gb|DV943371.1|DV943371
EST:     ATACAGGTTGGCTTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|91874366|gb|EB404323.1|EB404323
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATTTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|38229745|gb|CF920058.1|CF920058
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|211217164|gb|FL385248.1|FL385248
EST:     ATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|213173188|gb|FM191133.1|FM191133
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|32863787|gb|CF003469.1|CF003469
EST:     TTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: TTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|67022300|gb|CO451049.1|CO451049
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATCTGGGAGAATGGTA-TGTGCGTCAAGTTG
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGA-TGGTAATGTGCGTCAAGTTG
EST: gi|32849223|gb|CD988904.1|CD988904
EST:     ATCCAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|88756566|gb|DY540707.1|DY540707
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|24934254|gb|CA452472.1|CA452472
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|71758158|gb|DR956095.1|DR956095
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|32944796|gb|CF049615.1|CF049615
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|93280898|gb|EB673162.1|EB673162
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|211105793|gb|FL432184.1|FL432184
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|91053825|gb|EB164243.1|EB164243
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|76286900|gb|DV026468.1|DV026468
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|17931240|gb|BM268200.1|BM268200
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
EST: gi|78112559|gb|DV530953.1|DV530953
EST:     ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAG                         CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT
genomic: ATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGT

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: 235

CAGAGAAAATTGCAGACAAGGAATCAGAGTGCGATATCAGTATCCTGAATATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

CAGAGAAAATTGCAGACAAGGAATCAGAGTGCGATATCAGTATCCTGAATATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

CAGAGAAAATTGCAGACAAGGAATCAGAGTGCGATATCAGTATCCTGAATATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 191

CAGAGAAAATTGCAGACAAGGAATCAGAGTGCGATATCAGTATCCTGAATATACAGGTTGGCCTTATCCGTAAAGCATGGAAGCATCCATCTGCTGACAGgtgctgtatt ... gaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcagtgcttatgttatagtattcaacctaacgttctgattgatgaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT
         ttatgttatagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgtattttcactcttctgcaacacttagaatttctctgtattttcactcttctgcaacacttagaatttctctcagtgcttatgttatagtattcaacctaacgttctgattgatgaccgaccagCCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG