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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttccttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG

Basic information

species Zea mays
transcript GRMZM2G143253_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g22580.1 (Oryza sativa), 3'ss of exon 4
gtatttccttcttgcc--aagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG
||| ||  ||||| ||  |||   | |   || |  || |  |||| |||||   ||  || ||||| | ||       | ||  | | ||| |||||||| |||||||| || || ||||||||||||||||||||||||||  | ||||| || || |||||||| || ||| | ||||| ||| |||||||  
gtaattt-ttcttaccataagaatttttttacgtgatcaa--ttgtatgctgatgcaagtgcgctaagatgag----atagttcacttgcattcagATGTCAGATCCTCTTACTGCTCTGATGCATGCTGTTCAAGTGATGAATCTTCTCAAGACATTGATTCTCAAGACGCTTAGAGAACGTGAGCATGATGAAA

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G02720.1 (Glycine max), 3'ss of exon 3
---gtatttccttcttgccaagtcctctaacacat---cgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
    |||||   |      | |   |  | |  ||   | |  |   | | |   ||   |  ||  |||     ||        | |  |     ||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||| ||||| ||  | ||  | || |||||| | |||| |||  |  |      
gccatattttgcttacagtaggctatagatcttatgcacatgaaaactatgtatagttgaaaatggtctattgctaattcatctgtgtctcctggaacagATGTCTGATCCTCTAACAGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTCATCATGAAGACACTTAGAGAACACGAACA-AACAGCAA

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G17070.1 (Glycine max), 3'ss of exon 3
-gtatttccttcttgccaagtc------ctctaacacat-cgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctcc--atacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
  | |||   |    | | |        |||| |  ||   |   ||   |  |||||  | |       |  | |   ||||    ||| |||||    ||||||||| |||||||| || || ||||||||||| ||||||||||||||||| ||||| ||  | ||  | || |||||| | |||||||| ||  |      
catgttttgcttacactaggctatgctactcttattcacatgagaactacgaatgctggaaaatggtctgtttctaattcatc----tttgcctcctggaacagATGTCTGATCCTCTAACTGCCCTGATGCATGCGGTTCAAGTGATGAACTTACTCAAGACACTTATCATGAAGACACTTAGAGAACGCGAAGA-AACAGCAA

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G03100.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatttccttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG
        |     | ||||   |          |  |      |  ||| |    |    ||||||      ||     ||  ||   |  ||||| | |||||  | || || || ||||||||||||||||||||||||||||| || ||  | ||    || |||||    ||||| || ||  ||| | 
-------gtaaaaacaaagttaacctttgttcaatgaataagaatcactgagtagtt---actaacatttgattcttgcattctctaactgtagATGACAGATCCATTAACGGCTCTTATGCATGCTGTTCAAGTGATGAACTTGCTTAAGACTCTTATCACAAAGACACTAGCTGAACGGGAAGAAAATGCTA

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
---gtatttccttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG
   |   ||   |||||  || |    |     | |     | ||| |   || ||      |    | ||   | |     |||   | ||  |||||||| |||||  |||| || |||||||||||||||||||||||||||||||| || ||| | ||    ||||||||  ||||||| || ||       |
gttgatattaaatcttga-aaatttcttgttttagctaatgctttggtccatg-gatttcaataaatagaactccttttttgtttgatttcac-cagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------gtatttccttcttgccaa-gtcctctaacacatcgtcgacc-ttgtttgctgt-----gacacttg---tgctaacaagaac-------------atcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
                                                                            || ||| ||  |   |   |  |  ||   || | ||||   | ||||| |||     |    | |   || | || |                 ||   | |||    || | ||||||   ||||| || || || ||||||||||| |||||||||||||||||| | ||||| || |||||    ||| |   ||| || || |   |   || 
gtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcagATGGTTGATCCGCTAACGGCTCTGATGCATGCCGTTCAAGTGATGAACTTGTTGAAAACTTTGATTCTACGCACATTGAAGGACCG-GAAGGCTACTTTGC

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S159_36V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------gtatttc-----cttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaag-----aacatcgaaattttcctccat-----acagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
                                                                              ||| ||      ||    | | ||   ||||    |||   |    | |||| ||| |  |||||  ||  |||     |||||   || | |  | |||      |||||| | || ||  |||||||||||||||||||||||||||| ||||| |||||||||||  | ||||||   || ||   ||| || || |     | || 
gtatgtgatgtcgctgcaattgtgcgcctccccaaacttgtgacacttttcttaccagacttgtagagattcggtcctgtagttagcagactctccgactagatttctacgtgatctaaggaagtatttg-tgttaagcttgttatatgaagtgaataacatattaactatgattcattacttgcagATGGCTGACCCATTGACAGCACTGATGCATGCTGTTCAAGTTATGAATTTGCTCAAAACTCTGATTCTCCGCACTCTCAAGGACCG-GAAGGCCTCGCTGC

upper sequence: GRMZM2G143253_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------gtatttccttcttgccaagtcctctaacacatcgtcga----ccttgtttgctgtga--cacttgtgctaacaag---aacatcga--aattttcctccata------cagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG-
                                                                                    | | | |  | |  || || ||  |    | ||| |     || |||||   |||   || ||||  ||  | |   |||||  |   |  || || |||       |||||| | ||||| |||||||| |||||||||||||||||||| |||||||||||||||||  | |||||    |||||   ||| ||  | |   |   || 
gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtgtaacatttattgacattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCG-AAAGGCCACTTTGC

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|78105267|gb|DV523685.1|DV523685
EST:     AGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAG                         ATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTTCA-GTGATGAACTT
genomic: AGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAGgtatttcctt ... ctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTT-CAAGTGATGAACTT
EST: gi|211074489|gb|FL413463.1|FL413463
EST:     AGATGAATGCAAGADATGTTGCCATGGTTTTTGCACCAAATATGACACAG                         ATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTG
genomic: AGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAGgtatttcctt ... ctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTG

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: 111

TTGGGTCGTTGAGCTCATGGCTGATGTTGTTGAGGAAGAGGAGTCGAATAAGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAGgtatttcctt ... ctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 5

TTGGGTCGTTGAGCTCATGGCTGATGTTGTTGAGGAAGAGGAGTCGAATAAGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAGgtatttcctt ... ctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG


Block sizes: 45 (upstream exon), 29 (downstream exon)
Score: 12

TTGGGTCGTTGAGCTCATGGCTGATGTTGTTGAGGAAGAGGAGTCGAATAAGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAGgtatttcctt ... ctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG


Block sizes: 42 (upstream exon), 8 (downstream exon)
Score: 1

TTGGGTCGTTGAGCTCATGGCTGATGTTGTTGAGGAAGAGGAGTCGAATAAGATGAATGCAAGAAATGTTGCCATGGTTTTTGCACCAAATATGACACAGgtatttcctt ... ctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG
                    tgctaac  putative branch site (score: 1)
                                        ttttcctccat  putative PPT
                                     aaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttccttcttgccaagtcctctaacacatcgtcgaccttgtttgctgtgacacttgtgctaacaagaacatcgaaattttcctccatacagATGTCCGATCCTCTGACAGCACTGATGCATGCTGTTCAAGTGATGAACTTGCTCAAAACCTTAATTCTCAAAACACTTCGGGAACGCGAGGATGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG