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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatagatcgataatgatcatttggcatccttcatggacttttggttccttgattgttttttagtttcatgctttgattaattttattgtgtacatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC

Basic information

species Zea mays
transcript GRMZM5G816609_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 21
gtaagt--atagatcgataatgatcatttggcatccttcatggacttttggttccttgattgttttttagtttcatgctttgattaattttattgtgtacatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC
||||||  ||| ||| | ||||||| |||   | |  |  |  | | |    | | || |||| | | |  | | | | |  ||| |    ||| || |  |  |||||| ||||||||||| || ||||||||||| || ||||| |||||||| || ||||| |||||||||||  | ||||| ||||||||
gtaagttaataaatccacaatgatccttttaaacctgtgctccattctgttgtacctggttgtatataa--tgcgtacatatattgacaaaattttgcatgtattcagGTAAGAATTGCTCAAGGACTTGTTCACCTTGGGAAGGGTTTGTTGACTCTCTCTCCATACCATTCTGACCGGTTTCTACTTTCCCC
















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|67025197|gb|CO453946.1|CO453946
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|87157733|gb|DY402522.1|DY402522
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|31361134|gb|CD445491.1|CD445491
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|78179098|gb|DV549471.1|DV549471
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|12046100|gb|BF728239.1|BF728239
EST:     TCGCAATCTTTCAAGTGTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TCGCAATCTTTCAAGT-TATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|89763994|gb|DY690961.1|DY690961
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|26559722|gb|CA831957.1|CA831957
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|67013648|gb|CO442397.1|CO442397
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|6760600|gb|AW324699.1|AW324699
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGNTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|67041940|gb|CO468195.1|CO468195
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|71764383|gb|DR962320.1|DR962320
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
EST: gi|22819353|gb|BU499443.1|BU499443
EST:     TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCGGCTCATCTGTTTTGT                         GTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT
genomic: TTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTT

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), 49 (downstream exon)
Score: 206

ATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

ATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

ATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

ATTGGGTTTGATTGGTGCTGGCACAAACAATGCCAGAATAGCTGCCATGCTTCGCAATCTTTCAAGTTATTACTACAAAGAAGCAGCTCATCTGTTTTGTgtaagtatag ... acatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgattgttttttagtttcatgctttgattaattttattgtgtacatcatcagGTTAGAATTGCTCAGGGCCTTGTTCACCTCGGAAAGGGCTTGTTGACCCTTTCTCCGTACCATTCTGATAGATTTCTTCTTTCCCC
                            gattaat  putative branch site (score: 166)
                         tttgattaattttatt  TA-rich tract