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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaactatagtttctaattatacagacaaaaaatctccatagtttttttttcctaagaaaagtcgtgctggtttacttggtttttgtctgtcaaactatgacagatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG

Basic information

species Zea mays
transcript GRMZM2G021846_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 20
gtaaaaactatagtttctaa--ttatacagacaaaaaatctccatagtttttttttcctaagaaaagtcgtgctggtttacttggtttttgtctgtcaaactatgacagatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG
||  || | ||   ||||||  |||| |||| ||||| | | || |||| |||   | |    || |   ||  |   || |   || |          || |  || |  ||||||   |             |||||   |||| |  ||| || ||| || |||||||| || ||||| ||||||||||||||||| |||||||| || || || || || |||
gtttaatc-atttcttctaatattattcaga-aaaaacttttcacagttctttagac-tgcacaatgcaatg--gaaataatcaattct----------accagtac-gtcttcagtcttca------------ctaacttgtgatttggtaa-aatcctcagACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG
















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|211078223|gb|FL340045.1|FL340045
EST:     CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAG                         GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT
genomic: CTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGT




















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: 46 (upstream exon), 49 (downstream exon)
Score: 63

GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 53

GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

GTCACGAAAGAAGGACAAGCTAAGATACCGCTACCCCCGTGGAGAATCTTACCTCGATGTGATACAGAGgtaaaaacta ... taacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttcagttcccgtgtaactataccctaacagctgatgtcataataacccttagGCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAG
                                          taataac  putative branch site (score: 110)
                                                ccctt  CT-rich tract
                                       tcataataa  TA-rich tract