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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

Basic information

species Zea mays
transcript GRMZM2G069631_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 6
-tgaatgagttaa-tgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
 ||  ||||||   ||   ||    |  |    | |  | ||| ||      |    | |  |  | | | ||||||||| ||||  |||||||   | ||| || || || || | ||||||||||||||||||||||||||| ||||||||  | ||||||||||| || |||||||| |||||||||||||| ||||||
ctgtgtgagttctctgaacctataatactacctgcttctgtatattttcaaatca--tgagcatgaagctaataccatgttctcatattgttttacacccagTGACGGGGAGACATACATATCAGCAGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAACCAAAGCTTTAATATTGTTGATGTGAAGCCTGCA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 6
-----tgaatgagttaat-gtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
     || |||  ||  | |   |     ||||||||  | | ||| ||| |||      | |   |  |   |   || |||   |   ||    |   |   |||||||| ||||| ||||||||||| |||||| | |||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
tttcatgtatgttttttttgcacccttactttttttgtctatcatacttttctg---aaatctg--atcaaatttggactatggtat-gtttcaaatatctgctagCGATGGCGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 6
----tgaatgagttaatgtggctgagttttttttgga--tcttatattttgctgcctgggtttattactatggtgataccatgtc-ctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
    ||| |  ||  |  | | |    |||||||  |  | | ||| ||| ||   |     |   | |  | || |   ||||  ||||  || | |       |||||||| ||||| ||||||||||| |||||| |||||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
tacgtgattttgtgcacattgtttttatttttttaaaattttcatagttttctagatactgatcaaatttggatggtgttatgttgctcatattttct-------agCGATGGTGAAACTTTCATATCAGCTGATGATTTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 6
tgaatgagttaatgtggc-tgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
|  |||  |  || |     |   || |||| | |  | |||  ||||     |   | | |  |   |   || |||   |   ||    |   |   |||||||||||||| ||||||||||| |||||| | |||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
ttcatgtatgcattttttgcgcccttatttttgtttgtctatcatgcttttctgaaatctgatcaaatttggactatggtat-gtttcaaatatctgctagCGATGGAGAAACTTTCATATCAGCTGATGATTTACGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G42800.2 (Glycine max), 3'ss of exon 6
tgaatgagttaatgtg-gctgagttttttttggatcttatattttgctgcctgggtttattacta-tggtgatacc---atgtcctcactttgtt--ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
        || ||||   |    |||| |    || || | |||   | | ||| |||||   || || | | |     |||   | |  ||| |  |   |  ||||||||| ||||| ||||||||||| ||||||||||||||||| ||||||||  | |||||||||||||| || ||||| ||||||||||| || ||||||
-------ctttatgtctacatgattttgtgcacattttttttttaatttcatggttttatagatactgatcaaatttggatggtgttatgttgctcatatcttccagCGATGGCGAAACTTTCATATCAGCCGATGATCTGCGAATAAATCTTTGGAACCTGGAAATTAGCAATCAAAGTTTTAATATTGTTGATGTAAAGCCTGCA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 6
tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtt-tattactatg------gtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
    | | |   | || |  |  | || ||| ||| || ||||  |  | ||  ||  |||  | ||      ||| ||     || |  | ||  ||   | |||| || |||||||| || || || || |||||||||||| |||| || |||||||| ||||||||||| ||||| || || ||||||||||| || ||  ||
----ttattctctttgtcgaaaatcttgttg-atcctaaatttcacaacttgtattgcattgttttgttccttgtggtaatgaatcgttcccttaatt--gttacagTGACGGAGAAACCTTTATTTCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 8
tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
|  | |     ||      |      || | ||| |||  |   | |   |   || |||  ||  ||  | |           ||| | || |    ||||| || ||||| || || || || |||||| ||||||| || ||||||||| | |||||||||||||| || || || ||||||||||| || ||||| 
ttcaagttcctatccaaacggacaccttgttgatattagctcgagttctatactttcattgataatgttctgctcctaataatttttctcttataattagCGACGGCGAAACATTTATTTCTGCTGATGATTTGCGAATTAATCTTTGGAATCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTCAAGCCTGCG

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 6
tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgt---tttgttcaca-gCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
   |||     || |     |   | || |  ||  | |    |||    |  ||   ||   |       |     | || | ||| |   ||  ||| || | |||||||| || ||||||||||| |||||||| || ||||||||||||||  | |||||||||||||| || || || |||||||||||||| ||| | 
-acatggagccatattatccacactattctacatactgt---ctgcacttttagtcacttgtaagaaattaatagactactaattttatcctttcattctcaagTGATGGAGAGACATTCATATCAGCTGATGATCTACGCATAAACCTTTGGAACCTGGAAATTAGCAATCAAAGTTTCAATATTGTTGATGTGAAGCCTACT

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 6
tgaatga--gttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcc-tcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
 ||| ||   |||  |   |   | |  |  |   |  | |||||  ||   | || | |  | | | |||| |   ||    |   ||   | | |   ||| ||||| ||||| || |||||||| |||||||||||||||||||||||||| || ||||||||||| || ||||| || |||||||||||||| ||||||
-gaaagactattatggaaacaatgctaatggtaacttgtttatttctcttatttgggt-acgatt-tagtgaaattttgctgattgtttctctctctctccagTGATGGTGAAACATTTATATCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCA

upper sequence: GRMZM2G069631_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 6
--tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
  |  || || |    || |   | ||   | |  || | |   |  |    |     ||||   | | | |    |    |    | | ||   || | || ||||| ||||| || |||||||| |||||||| || ||||| || ||||| || |||||||||| ||| || || ||||||||||||||||| ||||||
gttatattagctgg-atgtcctggattgcatggtctccttttgctaacatattcatgatattgaca-gatcacttaacactccttttcttttccatttatagTGATGGTGAAACTTTTATATCAGCTGATGATCTCCGGATAAATCTCTGGAACTTGGAAATTAGCAGTCAAAGTTTCAACATTGTTGATGTGAAGCCTGCA

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|211079477|gb|FL398611.1|FL398611
EST:     GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAG                         CGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
genomic: GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
EST: gi|211374954|gb|FL429396.1|FL429396
EST:     GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAG                         CGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
genomic: GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
EST: gi|67012325|gb|CO441074.1|CO441074
EST:     GTATATGCCCATGCCCATGACTACCATATTAATTCCATCTCAAATAATAG                         CGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
genomic: GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
EST: gi|71772341|gb|DR970277.1|DR970277
EST:     GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAG                         CGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA
genomic: GTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAA

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: 102

GTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

GTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

GTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GTTACAGGCCAAGAATTTACTCATGTTGCGAGAAGCAGACGTGTATATGCCCATGCCCATGACTACCATATTAATTCCATTTCAAATAATAGgttagtttcc ... ttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA
                                tcctcac  putative branch site (score: 100)
                                tcctcactttgtttt  CT-rich tract
         tttattactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatgagttaatgtggctgagttttttttggatcttatattttgctgcctgggtttattactatggtgataccatgtcctcactttgttttgttcacagCGATGGAGAAACGTTCATATCAGCAGATGATCTGCGAATAAACCTTTGGAATTTAGAAATTAGCAATCAGAGCTTTAACATTGTTGATGTGAAACCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT