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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC

Basic information

species Zea mays
transcript GRMZM2G147145_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g49810.1 (Oryza sativa), 3'ss of exon 7
gttagtttaatgcatc-ttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaat-tatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
|| |||  |||  |   |||||  ||||| |   || ||||            || ||||||   ||  | ||||        | |  || |  |   |   ||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||| || |||||||||||||||||| ||||||||||||| ||||| |||||||
gtaagtgcaatctagagttcaatttggaattgcaatttcttgg----------caatgactgagaaacatgtattcggtaaaaactgctcatttttctaccatgcagGAGCCTGAGAAACATGTATTCCATCTTGTTACTGACAAGCTGAACTTTGGAGCAATGAACATGTGGTTTTTGTTGAATCCACCTGGAGATGCGACAATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------gttagtttaa---tgcatctt-caagctggaaatatgatctcttcattgtttgtacc--attgactggtcaattatattacact-------------cttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                            || |||     ||||   | ||| | ||| ||||  | | |     ||   | ||  | | | |    |||   |||| |||             ||||| ||| |  ||  ||  |||||||| |||   || ||||| ||||| ||||||||||| ||||| || ||||| ||||||||||||||||||||| ||||||| |||||  | || |||||| 
gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
-----gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
        | | |  ||||| |  ||| || |  ||||||   ||  |   || |||  || |     ||      | | |   || || || |  ||  ||  |||||||| |||  ||| ||||| ||||| |||||||| || ||||| || ||||| |||||||||||||||||| |  | || || ||||   | || |||||||
gcaccaaaaatatcgtgcatgtgaaag-tgtatctatgat---ttagtaaattatacttttaa--aaccag--gcctcataactttgttattgt--cttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------gttagtttaa---tgcatctt-caagctggaaata---tgatctctt---cattgtttgtaccattgactggtcaattatattacactcttatttttct---------tgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                             || |||     ||||   | ||| | ||| |||   || |  |||   |||   |   |  ||  |      ||||| | |   |  | ||| |  |         |  |  ||  ||| |||| |||   || ||||| ||||| ||||||||||| ||||| || ||||| ||||||||||||||||||||| ||||||| |||||  | || |||||| 
gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
--------------------------------------------------------------------------------------gtta-gtttaatgcatcttcaagctggaaatatg---atctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                                         | | | ||   ||| |  |  || || | |    ||   ||  |   || ||  ||| |      ||  |     ||    |   |||||  ||  ||  |||||||| ||    ||  |||| ||||| ||||||||||| ||||| || ||||| ||||||| |||||||||| |  | || || |||||  | || |||||||
gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaa------aaccaggcctcataacttagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
     ||  ||          |       || ||   |   |  |    |  |||    |  ||  || |  | ||||    ||  |  | |  |  ||| |||||| || |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||| ||||||||| || |||| || || ||  | ||||| ||||
----tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcctttttcattcactaagtttgctaataccctcgatt-gcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S251_8V6.1 (Physcomitrella patens), 3'ss of exon 8
gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattaca---ctcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
     | | |   | | |    ||       |  |   || |  | ||  |  ||   ||  ||  |||| || ||   |     | ||   |||| |     ||||||| ||    || ||||| |||||| ||||||| ||||||||||||| ||||||||||  ||||||||| ||||| || || || || | ||| || ||||
---gctcttacatagcataggtctattttctttttagttttagcggtttgagaataagcttctctgttattttgcaaggcctaagtgttatctgctgt-----tgcagGATCCCAGTAAGCATGTCTTTCATGTTGTTACAGACAAACTGAACTATGGGGCCATGCGCATGTGGTTCTTGCTCAACCCCCCCGGTGCTGCTACCATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------gttagtttaatgca----tcttcaag----ctggaaatatgatctctt-cat-tgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                ||  ||||| ||     || | |||    |||   | ||||  |  |  || || | |     |  |  | ||  | |||  | || | |||||    |         ||||||||||| || ||||| || |||||  ||||||| ||||| || || ||||| |||||||  |||||||||||    ||||| || |||| |||    || |
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC

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|60341609|gb|DN208582.1|DN208582
EST:     ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAG                         GAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
genomic: ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
EST: gi|32932150|gb|CF036962.1|CF036962
EST:     ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAG                         GAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
genomic: ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
EST: gi|5928665|gb|AW056062.1|AW056062
EST:     ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAG                         GAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
genomic: ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
EST: gi|47961954|gb|CN844663.1|CN844663
EST:     ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAG                         GAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG
genomic: ATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGG

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: 200

TGAGAACCTGGAAAATCCTGATCTTTACCATTATGCTCTTTTCTCGGACAATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

TGAGAACCTGGAAAATCCTGATCTTTACCATTATGCTCTTTTCTCGGACAATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

TGAGAACCTGGAAAATCCTGATCTTTACCATTATGCTCTTTTCTCGGACAATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

TGAGAACCTGGAAAATCCTGATCTTTACCATTATGCTCTTTTCTCGGACAATGTTTTGGCAGCATCAGTTGTGGTCAACTCAACCATCATGAATGCTAAGgttagtttaa ... aaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
  cattgac  putative branch site (score: 176)
              aattatattacactct  TA-rich tract