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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG

Basic information

species Zea mays
transcript GRMZM2G168510_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g10784.2 (Oryza sativa), 3'ss of exon 10
-----tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
     |||   ||| || | |        |  | |   || |||   |  || |||  ||    | ||  || |||| | || |    | ||| | |||||||||||||||||||||||||||||||| || ||  |||||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||||||||||
agttttttgaacaccatgttaccgtcccttcctcaaatatctatg--tatttgtgcaagtagacggtt--gtcaaattgtgcatatttg-gttctcttttgtaagCTTGATGGTGGAGGTGTTGCAAGTGGGGGCTTACGAGAACTAATACCATGCATCGCAAGGACTTCTGTTGCTGTCGGAGTTGATGGTATTTTCATGGAG

upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G48370.1 (Glycine max), 3'ss of exon 9
tttcgtcacaatttcagaactagcttatgatga--atttattg---ttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG-
     | ||   |  ||  ||||||| | |  |  | ||  ||   |  | ||| |   | ||     | ||| | | |          || |||   |  | || | ||||| ||||||||||| || || || || |||||||||||||| ||||||||||||||  | ||||| ||||| || ||||| || ||||||||| 
-----tgacttctgtagttctagcttttaaaaataactttctgaaatgacctttccaaatcttacacctggttcattggattaaaattctgcttt-catgattagtTGGATGGGGGAGGTGTTGCTAGTGGAGGTCTTCGAGAACTAATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAGG

upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38010.1 (Glycine max), 3'ss of exon 10
tttcgtcacaatttcagaactagcttatgatgaatttattg---ttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgta-agCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
     | ||   |  ||  ||||||| | |  || ||  ||   |  | ||| |   | ||     | |||   |            || ||| || |||| || | ||||| |||||||| ||||| || || || |||||||| ||||| ||||||||||||||  | ||||| ||||| || ||||| || |||||||||
----ctgacttctgtagttctagcttttaaataactttctgaaatgacctttccacatcttacacctggttcgttgaattaaaattctgctttcttgtgtatagTTGGATGGAGGAGGTGTGGCAAGTGGAGGTCTTCGAGAACTGATACCTTGCATTGCAAGGACAGCAGTTGCCGTTGGAGTGGATGGGATCTTCATGGAG

upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G79500.1 (Arabidopsis thaliana), 3'ss of exon 10
-tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
 | |  ||    ||| | || || ||| | ||   |||||| |||       |  |       |   || ||   |      |  |   || |  |||| | | |||||||| ||||||||||| || || || || ||  ||||||| ||||||||||| ||  |||| || ||||| || ||||| ||||||||||||
gtatgatcct--tttaaaaagtaactttttat---tttatt-ttgaagccagcaataaccaaatagtttgaacacga----acaatacattctgatgta-gTTGGATGGTGGTGGTGTTGCAAGTGGAGGCCTTCGCGAGTTAATACCATGCATTGCAAGAACAGCTGTAGCAGTTGGCGTCGATGGAATTTTCATGGAG

upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G16340.3 (Arabidopsis thaliana), 3'ss of exon 10
tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagtta-aatcgggctttgc-----cgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
    ||       | ||||| |   | |||  ||||||         |||  | | |     | | | | ||| || ||   |     | |   || |||    || | |||||||| |||||||| || ||||| || || ||| ||||||| ||||| ||||| ||  | || ||||||||||| ||||| ||||||||||||
----gtatggtcattagaacgatgctctgagtaatttaagaaaatgcttggtgttttaaagctaaatcagaattggtctaaactcaaacataccttgtttatatagTTAGATGGTGGGGGTGTTGCTAGTGGTGGCCTTCGCGAATTAATACCATGCATAGCAAGAACCGCCGTAGCTGTTGGTGTCGATGGAATTTTCATGGAG

upper sequence: GRMZM2G168510_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 9
tttcgtcacaatttcagaactagcttatgatg--aatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
 |   |   |||  || |      ||  ||||   |   ||| ||   ||  |              | | |    |   |    || | || ||     |||| || || ||||||||||| || || || || || ||| | ||||| |||||||| |||||  | ||||||||||| || ||||| ||||||||||||
-taaatttgaatgccacataatattttagatgctgagccatt-ttttcttaacaaaaaaaaaacaccgatgatgaagagctaaaggtctatttttcaaacagCTGGAAGGCGGAGGTGTTGCCAGTGGAGGTCTTCGTGAATTGATACCATGCATTGCGAGGACAGCAGTTGCTGTTGGAGTGGATGGAATTTTCATGGAG

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|31362214|gb|CD446571.1|CD446571
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|60359317|gb|DN226290.1|DN226290
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|60340487|gb|DN207460.1|DN207460
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|71307283|gb|DR789816.1|DR789816
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|76910910|gb|DV164091.1|DV164091
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|5871261|gb|AW017732.1|AW017732
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|16917526|gb|BM073324.1|BM073324
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|60400102|gb|DN232909.1|DN232909
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|74236360|gb|DT644274.1|DT644274
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|60398159|gb|DN230975.1|DN230975
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|5325089|gb|AI783280.1|AI783280
EST:     GTTGTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTTGTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|50323771|gb|CO518897.1|CO518897
EST:     ACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: ACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|211183212|gb|FL204166.1|FL204166
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|71763878|gb|DR961815.1|DR961815
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|211051797|gb|FL187615.1|FL187615
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|33101621|gb|CF061581.1|CF061581
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
EST: gi|4730747|gb|AI649913.1|AI649913
EST:     GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAG                         CTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC
genomic: GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGC

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: 45 (upstream exon), 49 (downstream exon)
Score: 228

GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 128

GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 152

GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 103

GTAGCTGATGTAACACATGCTCTACAGCAACCAGCTGGAAGAAAGgtatctttac ... attttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG
                                         ttttatttt  CT-rich tract
           tttgttttagttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgtcacaatttcagaactagcttatgatgaatttattgttgcttttgccggtgtttgttttagttaaatcgggctttgccgtgttttattttgtaagCTTGATGGTGGAGGTGTTGCAAGCGGTGGGCTACGAGAACTAATACCGTGCATTGCAAGGACTTCTGTTGCTGTTGGTGTTGATGGTATTTTCATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA