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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcctgctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg...

Basic information

species Zea mays
transcript GRMZM2G052926_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g36120.1 (Oryza sativa), 5'ss of exon 6
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcctgctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg----------
|| ||||| ||||| ||||||||||| |||||| ||||||||||||| |||||||||||||||| |||||||||||||||||||||||| |||||||||||| |||||  ||     ||||| ||||  ||  ||| |||  |   |  || |||  ||       || | |  ||||| |||||||||||| ||||  |          
ATTCACCACATGATGTATCCTATAACTGTGGAGGTTCTACATCAAGTTTTCAAAGCTTATGGATATGTGGAGAAGATTGTCACATTTCAGAAGTCAGCTGgtcagattccccca---tctctctctcactccgcacacacatgcatagttgatatggat------gttacttagcagat-gcatgtgaatggcaaggctgatttatcaat

upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G36770.1 (Glycine max), 5'ss of exon 5
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt-cctgctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg--
 | || || ||| | |||||||| || |||||  | ||  ||||||||||     |  |||||| |||||| |||||||| |||||||| |||||||||||| ||||| |  | | | ||||  | ||| |     |   |   |  || |  | |   |||   || |   | ||    |  ||     |  ||   | |  
GTTCATCACATGTTGTATCCTATGACTGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctgtcagatttctccctttctcttctttccatcctattaacatttt-tgtgtttctggactt--taactaggtagattgaggttatatttttgtc

upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA20G30820.1 (Glycine max), 5'ss of exon 6
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcct-gctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg-
 | || || ||| | |||||||| ||||||||  | ||  ||||||||||     |  |||||| |||||| |||||||| |||||||| |||||||||||| ||||| ||   | | ||||  | ||| |     |   | |    | |   | |   ||    || |       || | || || |  |  ||   | | 
GTTCATCACATGCTGTATCCTATGACAGTGGATGTGCTGTATCAAGTATTTTCTCCCCATGGATCTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttctccctttctcttctttccatccctattaacatttttgtgttcctagactttaac-taggtagcttgaggtta-tatttttgt

upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G08870.1 (Glycine max), 5'ss of exon 6
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcct-gctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg-
 | || || ||| | ||||||||||||| |||  | ||||||||||| ||     |  ||||||||||||| |||||||| ||||| || |||||||||||| ||||| ||   | | |||   ||||| |  |    |        |  |  | |   | ||  |   || | || |  || || |||      |  ||| 
GTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGATTGTAACATTCCAGAAGTCAGCTGgtcagattctctcagatttcttcctctctctttcttttcctattaagattttttttttgtctta-ggggccttcacggggtgaat-tgaggatatatttggt

upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G27970.1 (Glycine max), 5'ss of exon 4
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcct-gctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg-
 | || || ||| | ||||||||||||| |||  | ||||||||||| ||     |  ||||||||||||| |||||||| |||||||| |||||||||||| ||||| ||   | | |||   ||||| |  |    |        |  |  | |   ||||  |   || | |  |  || || |||      |  ||| 
GTTCATCACATGCTGTATCCTATAACAGCGGATGTGCTACATCAAGTGTTTTCTCCCCATGGATTTGTGGAAAAGATTGTAACATTTCAGAAGTCAGCTGgtcagattctctcagatttcttcctctctctttcttttcctattaagatttttt-tttgttttagggggccataatggggtgaat-tgaggatatatttggt

upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv18s0072g00310.t01 (Vitis vinifera), 5'ss of exon 5
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcct-gctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg-
|| || ||  || | || ||||||||||||||| | || |||||||| ||     || |||| |||||||||||||||||||| ||||| |||||||||||| || || | |  | | ||||| | | | || |   |  |  ||    ||       | ||  | |||| | |    | |      || | |   | ||| 
ATTCATCACCTGCTATACCCTATAACAGTGGAGGTGCTGCATCAAGTGTTTTCTCCTCATGGTTTTGTGGAGAAGATTGTCACGTTTCAGAAGTCAGCTGgtcagcttcttcaagttttctctctttatctctct-tgtgc-tgtctctctatctcttaattcttaattctcctttcaactcttgaggactagctggatggt

upper sequence: GRMZM2G052926_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv07s0031g02030.t01 (Vitis vinifera), 5'ss of exon 6
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcctgctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaa--tggtaaggtgg
|| || ||  |  | ||||| |||||||||||  | || |||||||| ||     || |||| ||||| |||||||||||||||||||||||||| || ||| ||||| | |   | | ||| ||||| ||   | |||       |  |  | |  ||||| | | |   ||  |  ||| |  | ||  |  ||   || 
ATTCATCACCTACTATATCCCATAACAGTGGAAGTGCTCCATCAAGTGTTTTCTCCTCATGGGTTTGTTGAGAAGATTGTCACATTTCAAAAGTCGGCGGgtcagattcttcaagttt-tctctctctatc-ttatgcattgtcttagttcttgtttattttattaatgattttgattttggagtttaagatactagaatgt

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|31361372|gb|CD445729.1|CD445729
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|93284255|gb|EB676519.1|EB676519
EST:     CAAAGCTTATGGATTTGTGGAGAAAATTGTCACATTTTAAAAGTCAGCTG                         GTTTTTAAGCTCTTATTCAGTATCACTCCGGGC-AAGAAGCTGGTGGA
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTC-GCGCCAAGAAGCTG-TGGA
EST: gi|67014377|gb|CO443126.1|CO443126
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|31358368|gb|CD442725.1|CD442725
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|76013333|gb|DT940503.1|DT940503
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|78087001|gb|DV515394.1|DV515394
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|31250253|gb|CD219277.1|CD219277
EST:     AAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAAGTCAGCTG                         GNTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: AAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAA-GTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|78080905|gb|DV509317.1|DV509317
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
EST: gi|32943654|gb|CF048473.1|CF048473
EST:     CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTG                         GTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT
genomic: CAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCAT

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), 48 (downstream exon)
Score: 226

ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 79

ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 85

ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 130

ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagatttt ... actgatgcagGTTTTCAAGCTCTTATTCAGTATCACTCGCGCCAAGAAGCTGTGGAAGCATTTGGTTCTTTGCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCACCATATGATCTATCCTATAACAGTGGAGATTCTACATCAAGTATTCAAAGCTTATGGATTTGTGGAGAAGATTGTCACATTTCAAAAGTCAGCTGgttagattttcctgctctctctatctctttcaccacgcacgcgtgcacctggtatacattttctgattcccttacagattgcatgtgaatggtaaggtgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctctctc