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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaaggaaatgattaactacaattttctgttcattcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC

Basic information

species Zea mays
transcript GRMZM2G076394_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaaggaaatgattaactacaattttctg---ttcattcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC
|| ||||   | | ||| ||| | |  |  || | ||     ||   |    |  |  |      | |      | |  ||   | ||    |  |||| || || || ||||| ||||| |||||||||||||||||   ||| || ||||| || ||||||||||| || ||||||||||||||
gtgagtt--gttagcttttctcggc--ttctggttcatcatatatagtcttctccacaattattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC

upper sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaaggaaatgattaactacaattttctgttcattcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC
||||||    |  || ||| ||  |   ||   |||||         ||     |  || || |||  |        | || |||   || ||||  |||||| ||||||| |||| |||||||||||||||||     |  || |||| ||| ||||| ||||| || ||||| || || ||
gtaagtcatttagtcatcttttagcttggtaattgcaccattcccattgtacagattgatataattttcc-----cgtttggtcaca-ttttagGTTGGCTATGTGTGGTATGAATGTATCTACAAGCTGGACAGGACCAGTTACAACATGTATCATCCGTACACATCATGGATCCCCATCAC

upper sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaaggaaatgattaactacaattttctgttcattcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC
|| ||||    | |  ||||| ||   | | |||   || |      |||  |||     |||   || |    | |||  |  ||| ||| |||  || || || ||||| ||||| || |||||||| |||||   |||||| ||||| || ||||||||||| |||||||||||||||||
gtgagtttg--ggttctctctggct--tatggat---cttatgtatttgatattattctgatgcccaagt----tgttccctatattgttc-agGTTGGTTACCTATGGTATGAATACATATACAAGCTTGACAAGGTTACATACAACAAATATCATCCCTACACATCGTGGATTCCAATAAC

upper sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttccatgatcttctcttgccagtgttgatgcactgactaggatgagtttaag-gaaatgattaactacaattttctgttcattcttctag-
||||||| ||||||| | |  |  |||| ||  |    |  ||     || |||||| ||  |  |||  || | |||  | ||| || || |||                                  |  || ||| ||||||| ||||| || |||||||||||||||  ||||||||| |||| |||||||||||| || ||||||||||||||
gtaagttgcatgatcctgtgatcacagtattattct--tatctgtttagattttaagtgacttttttatttatactttctttttcttttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC

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|6056529|gb|AW090919.1|AW090919
EST:     CTAAGGTGAGAGTGTTAATCAAGGGAACCATTGTTACAGCTTCCTTAATG                         GCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATAT
genomic: CTAAGGTGAGAGTGTTAATCAAGGGAACCATTGTTACAGCTTCCTTAATGgtaagttcca ... attcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATAT




















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: 36 (upstream exon), 14 (downstream exon)
Score: 2

GTTGAAAGATGGATGGAAAAGCTGGAAGAATCTGAGACTAAGGTGAGAGTGTTAATCAAGGGAACCATTGTTACAGCTTCCTTAATGgtaagttcca ... attcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 152

GTTGAAAGATGGATGGAAAAGCTGGAAGAATCTGAGACTAAGGTGAGAGTGTTAATCAAGGGAACCATTGTTACAGCTTCCTTAATGgtaagttcca ... attcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 280

GTTGAAAGATGGATGGAAAAGCTGGAAGAATCTGAGACTAAGGTGAGAGTGTTAATCAAGGGAACCATTGTTACAGCTTCCTTAATGgtaagttcca ... attcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 5

GTTGAAAGATGGATGGAAAAGCTGGAAGAATCTGAGACTAAGGTGAGAGTGTTAATCAAGGGAACCATTGTTACAGCTTCCTTAATGgtaagttcca ... attcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactaggatgagtttaaggaaatgattaactacaattttctgttcattcttctagGCCGGCTATCTGTGGTACGAATATATCTACAAGCTGGACAAACATACATATAACAAGTACCATCCCTACACGTCGTGGATTCCAATAAC
                       gattaac  putative branch site (score: 5)
                                   ttttctgttcattctt  putative PPT
                        attaactacaatttt  TA-rich tract