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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacccccagtttcagaatcttgttttcctcatgtttgggtgctctgatgttcatgcaattttgttgctgcgaaggctaattattcttttttggatgaactttaaaaaatgtcgctgtagtttttagtgggattttttttggcaacaaaatgcaactcatacctggctttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT

Basic information

species Zea mays
transcript GRMZM5G817439_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G817439_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g48530.1 (Oryza sativa), 3'ss of exon 11
gtttacccccagtttcagaatcttgttttcctcatgtttgggtgctctgatgttcatgcaattttgttgctgcgaaggctaattattcttttttggatgaactttaaaaaatgtcgctgtagtttttagtgggattttttttggcaacaaaatgcaactcatacctggctttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT
                                                                  ||       |||| ||  | |  | | | |||  |||        || |  |||| | | |  |   |        ||||||  ||  || |    |    | ||    |||||||| || ||||| |||||||| || |||||||| || || |||||||||||||| |||||| |     |        ||     |   | | |  |   |
-----------------------------------------------------------------attatcatagaggcaaa--aatagtatgttgatttact-------gtgccattgtactatattttacaacc------ggcaacttaacccatccatgatgacgattcttctgcagTTACAATGACCTTGATGCTCCGGACGAGGAAGTTACCGTTCTTGACTACAGAAGTTTGTAGAGCTTGCCCTGGTGTAATTGTAATTTGCCAATCACAACT
















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|110952186|gb|EE172238.1|EE172238
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|32838060|gb|CD977738.1|CD977738
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCCCTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|37398555|gb|CF636593.1|CF636593
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|211231311|gb|FL465072.1|FL465072
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|32908236|gb|CF013049.1|CF013049
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|32838176|gb|CD977854.1|CD977854
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|37394775|gb|CF634664.1|CF634664
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|149107323|gb|EE189204.2|EE189204
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|37389219|gb|CF631828.1|CF631828
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
EST: gi|50326202|gb|CO521328.1|CO521328
EST:     ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAG                         TTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG
genomic: ATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAG

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), 35 (downstream exon)
Score: 8

CACATGGCAATGCTGGAATGCTTGGGCCAATGATGGGTGGCCCAGCACCGATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT


Block sizes: 49 (upstream exon), 26 (downstream exon)
Score: 5

CACATGGCAATGCTGGAATGCTTGGGCCAATGATGGGTGGCCCAGCACCGATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 9

CACATGGCAATGCTGGAATGCTTGGGCCAATGATGGGTGGCCCAGCACCGATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 3

CACATGGCAATGCTGGAATGCTTGGGCCAATGATGGGTGGCCCAGCACCGATTATAGCTATGCCTCCAAATTTCCGCCATGATCCTCGCCGCCTGAGAAGgtttaccccc ... ttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtgggattttttttggcaacaaaatgcaactcatacctggctttggttgcagTTATAACGACCTCGATGCTCCTGATGAGGAAGTCACTGTCCTTGACTACAGAAGCTTGTAGGGTCCAGCACCTCCAGATACCCGTAGTCAAGTTTCCCGT
        atttttttt  TA-rich tract