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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatttcgtgcttcacaactagattggatttctcatttgtcttctacttacacgactacttttgccttctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 30
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 28
-------------------------gtatgttatttcgtgcttcacaactagattggatttctcatttgtcttctacttacacgactacttttgccttctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG
                           | | |   |  |  ||    |  || ||  ||  |||| |   |       |  | |  | |  || | || | |||||||||||| ||||| |||||||||||||| || || ||||| |||||||||||||| |||||||| |||||||||||||| || |||
gtatattacctttgtgtccggttttacaagatcaattttcatttgttaagaggttcaatccctcaatccccccaggaattgatggatgccattcctttttctttctagGTTCCGGAGGAAGAGAAAAATCTTGGTCCTTTTGATCGCTTGATTCATGTATACCATTTTACCAAAGACACTCAAAATCAGACG
















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|61118763|gb|DN559724.1|DN559724
EST:     AAAAGATTGAAAACATCAATGATCAGTACTG-ACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
EST: gi|78106266|gb|DV524684.1|DV524684
EST:     AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
EST: gi|76909980|gb|DV163634.1|DV163634
EST:     AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
EST: gi|60394863|gb|DN227732.1|DN227732
EST:     AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
EST: gi|211394943|gb|FL031667.1|FL031667
EST:     AAAAGATTGARAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
EST: gi|67014431|gb|CO443180.1|CO443180
EST:     CAATGATCAGTACTGGACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAG-AAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: CAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
EST: gi|67020350|gb|CO449099.1|CO449099
EST:     AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAG                         GTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA
genomic: AAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTA

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: 211

GTATTTGCACCAAATGAAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 74

GTATTTGCACCAAATGAAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GTATTTGCACCAAATGAAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GTATTTGCACCAAATGAAAAGATTGAAAACATCAATGATCAGTACTGGACACTGCGTGCAGAGGAGgtatgttatt ... ctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggatttctcatttgtcttctacttacacgactacttttgccttctatttctagGTTCCAGAGGAGGAGAAAAATCTTGGCCCCTTCGATCGTTTGATTCATGTATATCATTTTACAAAAGACACTCAAAACCAAACG
                     tacttac  putative branch site (score: 141)
                                ctacttttgccttcta  putative PPT
                                           ttctattt  TA-rich tract