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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcatgcccaatcttcattcctaactgcatgcgatgcctgattcacgcgcgccttcttttctatctaaaagtaaactactattgtgcagaaaaattcagtctgcttgtcttgtgctaatttgttcactaccttttgctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA

Basic information

species Zea mays
transcript GRMZM5G823629_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 2
gtaagagcatgcccaa--tcttcattcctaactgcat-----gcgatgcctgattcacgcg-cgccttcttttctatctaaaagtaaactactattgtgcagaaaaattcagtctgcttgtcttgtgctaatt-tgttcactaccttttgctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA
|||||| |||||   |  || ||| || |   || ||        ||||||  | | | || |   |   |   |     |||   |||||   |||||||| |||   ||||| | || | ||||||||||  |||   | |   | || |  | ||||||||||| |||||||| | ||||||||||  |||||||||||||| ||||||||||||||| ||||| ||||||||||||| ||||||||||| |||||
gtaaga-catgctataattcctcactcgtggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaa--ccagtcagatt-ttttgtgctaatgatgtgttccattgtgtgtttgtgcagCTACAACATTGACTGGATTGCATTTTGCAACCACAACCTTGATGACATTAGTAATGAAATGGTTGGGACATATTCAGCCATCCTATTTACCATTGCCAGA

upper sequence: GRMZM5G823629_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 2
gtaagagcatgcccaatcttcattcctaactgcatgcgatgcctgattcacgcgcgccttcttttctatctaaaagtaaactactattgtgcagaaaaattcagtctgcttgtcttgtgctaatttgttcactaccttttgctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA
                     |     || ||     | |   | ||| || |     |    |    |  |||  | ||    ||     |  |   | | |     | || ||||| ||||| ||        || |||||  ||||||||||||| |||||||||| ||||||||||  || || |||||||| ||||||||||||||||||||||||||||| || || || |||||| | |||||
-------------------gtacgataaattgataatgctttattatttactcatatgtgtgatcacttggaaagatgaatctgtaacaaactcagctactgaac--acatg-cttgtactaatatgggggtg--ctattgcttgtacagCTACAACATTGACTGGACTGCATTTTGCAACCACGACTTTGATGACATTAGTAATGAAATGGCTGGGATATATTCAACCGTCCTACTTACCAGTGCCAGA
















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|33095403|gb|CF055397.1|CF055397
EST:     TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTG                         CTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
genomic: TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
EST: gi|33093441|gb|CF053435.1|CF053435
EST:     TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTG                         CTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
genomic: TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
EST: gi|71436501|gb|DR817551.1|DR817551
EST:     TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTG                         CTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
genomic: TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
EST: gi|76015510|gb|DT942680.1|DT942680
EST:     TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTG                         CTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
genomic: TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
EST: gi|149089689|gb|EE178948.2|EE178948
EST:     TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTG                         CTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG
genomic: TATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAG

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), 47 (downstream exon)
Score: 157

GCAGCACTAGATGCTGGCGCATGGATGTTCAATGTCGTCACATCTGTTGGTATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA


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

GCAGCACTAGATGCTGGCGCATGGATGTTCAATGTCGTCACATCTGTTGGTATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA


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

GCAGCACTAGATGCTGGCGCATGGATGTTCAATGTCGTCACATCTGTTGGTATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 181

GCAGCACTAGATGCTGGCGCATGGATGTTCAATGTCGTCACATCTGTTGGTATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcat ... gctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattcagtctgcttgtcttgtgctaatttgttcactaccttttgctcctacagCTACAACACTGACTGGACTTCATTTTGCAATGACAACCTTGATGACGTTAGTAATGAAATGGCTGGGATATATTCAGCCATCTTATTTACCATTACCAGA
                      tgctaat  putative branch site (score: 181)
                                    ctaccttttgctcct  putative PPT
                         taatttgtt  TA-rich tract