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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattacctgaaggctaccattagcagttgctctaaggaaaattgtcattactttgatctcgttctgtaatcttcctggcagttaattccattatttgctgtgtggtttgatggttgatgtatgtccatattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA

Basic information

species Zea mays
transcript GRMZM2G008216_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 3'ss of exon 2
---------gtaaattacctgaaggctaccattag-cagttgctc-taaggaaaattgtcattactttgatctcgttc-tgtaatcttcctggcagttaattccattatttgctgtgtggtttgatggttgatgta-tgtccatattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA
          | | ||| |||        | | |  || ||| || | || | |  |||      || |  ||  | | ||| |   | |     ||| |   ||  |||| | |   | |       |||  ||  |||  |  ||| |||||||||||||||| || ||||| ||||||||||| || |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||| |
gtgaaatgctttatttatctgtcactgctcgtaaatcatttgttcatgagaatatgtgtatccgtttgggccttttgcgtgttaaacttcgaattgtttaccacaccattttcggatagctactcacattgtcgttctgttaaattttcagGCTTGCAAAAAGCTCGGAAAAATCGAGCTCTCAGATTGTGAAATTTACGCGTCTTGTGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGGA

upper sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 3
gtaaattacctgaaggctaccattagcagttgctctaaggaaaattgtcattactttgatctcgttctgtaatcttcctggcagttaat-tccattatttgctgtgtggtttgatggttgatgtatgtccatattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA
                                    ||   | |||   ||| | |  | | | |    || ||| | |     ||||| | ||| ||||  |   |  | | ||  ||     || || ||  | ||||||||  |||||||     ||||||| ||  | ||||| ||||| || || || |||||||| || |||||||||||||||||| ||||||| ||  |||
----------------------------------tgaaaccacatttatatttcctaaaccacatcacttattctacttatttcttaatatacatcattttgtacctcatgttataatttg---atatc-at-ctatagGCTTGTCAAAAGCTGAATCAAATTGAACTTGCTGACTGTGAAATCTATGCTTCTTGCGAGCCTTGTCCAATGTGCTTTGGTGCAATTCATCTTTCAAGAA

upper sequence: GRMZM2G008216_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv14s0030g01610.t01 (Vitis vinifera), 3'ss of exon 3
gtaaattacctgaaggctaccattagcagttgctctaaggaaaattgtcattactttgatctcgttctgtaatcttcctggcagttaattccattatttgctgtgtggtttgatggttgatgtatgtccatattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA
                                     |   | |||||  | | |          |||| ||            |   |||  | ||   || |||  | | ||| |||   |    || |  |  |||| || || |||||     |||||||||| |||||||| ||||| || || || || ||||| ||||||||||||||||||||  | ||||| ||  |||
-------------------------------------aactagattgtgctcattgaatgacaaatctgcaagtgattcacttctcttttcagtgatactctttgtt-tctcatgcttggaatgaaaccttcctgcagGCATGTAAGAAGCTCAATCAAATTGAGCTATCAGACTGTGAAATCTATGCCTCTTGTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAA

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|60395351|gb|DN228220.1|DN228220
EST:     TGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCG
genomic: TGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacc ... catattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCG
EST: gi|60396933|gb|DN229752.1|DN229752
EST:     TGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCG
genomic: TGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacc ... catattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCG

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: 91

AGTTGTCGTCTGTAATGACGAAGTAGTAGTCAGCTGCCATAACATGGTTCTGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacc ... catattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 206

AGTTGTCGTCTGTAATGACGAAGTAGTAGTCAGCTGCCATAACATGGTTCTGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacc ... catattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

AGTTGTCGTCTGTAATGACGAAGTAGTAGTCAGCTGCCATAACATGGTTCTGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacc ... catattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

AGTTGTCGTCTGTAATGACGAAGTAGTAGTCAGCTGCCATAACATGGTTCTGAAGCACACTGACCCTACTGCGCATGCTGAAGTAACTGCAATTAGAGAGgtaaattacc ... catattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaattccattatttgctgtgtggtttgatggttgatgtatgtccatattttagGCTTGCAAAAAGCTTGGGAAAATTGAGCTCTCAGACTGCGAAATTTACGCGTCCTGCGAGCCATGCCCAATGTGCTTTGGTGCAGTTCATCTCTCCCGAA
                                              atatttta  TA-rich tract