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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatag

Basic information

species Zea mays
transcript GRMZM2G177970_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177970_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g54020.1 (Oryza sativa), 5'ss of exon 10
GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatag
||||||||||||||||| ||||||||||||||||||||||||||| |||| || ||||||||||||||  ||         ||||   |   |||   ||||||  |      |     |||  | | |   | |||||   ||||    ||||||      |||   || | ||| || ||  |              
GTTCCTGAAGCCCTTATACCTCCAGCAGGGGCTCGTGTTATGTCCTTAACCGACGGTCTCTCCAAGgtagtta--------gccatactcattatcattttaatcctgatcacaaaaaatgaaactactaggactttttt--gttattaaattact------tat---tgaagtgtcattacacc--------------

upper sequence: GRMZM2G177970_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT2G25840.2 (Arabidopsis thaliana), 5'ss of exon 8
GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactg-tcctctatacatgtaatgtgatgacttctgttttggtgatag
 | || ||| | || || || | ||| || |||||||||||||| || ||||||||||| ||||||||  |      |  |     || | |  | | || |  | |   || || |  |    |  ||  |   ||     ||| | | | || || || || ||| ||  ||                          
ATACCAGAACCACTCATACCACAAGCTGGAGCTCGTGTTATGTCTCTTACTGATGGTCTTTCCAAGgtagt------atgttttcattcacagctactttaaggtttctggtcatttattttttc--tttctgcattcagcagttgcgtcactattggtcttcaatagataaaa--------------------------
















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|32944158|gb|CF048977.1|CF048977
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGTCTGCTCCTTCAGACCAATCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
EST: gi|32930432|gb|CF035244.1|CF035244
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGTCTGCTCCTTCAGACCAATCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
EST: gi|71449703|gb|DR830753.1|DR830753
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGCCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
EST: gi|32930572|gb|CF035384.1|CF035384
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGTCTGCTCCTTCAGACCAATCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
EST: gi|78120427|gb|DV538811.1|DV538811
EST:     TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAG                         ATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA
genomic: TTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCA

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: 48 (upstream exon), 48 (downstream exon)
Score: 134

GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 215

GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 63

GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 80

GTTCCTGAAGCCCTTATTCCTCCAGCAGGGGCTCGTGTTATGTCCCTAACTGATGGTCTCTCCAAGgtgattgaca ... ttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT