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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctatctcccatttttcagaatgaatttttatttggattaggttcattttttttgtgcaatgcaaagttcatgtcttagcaccatttgaattttagaaaccaacttattttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG

Basic information

species Zea mays
transcript GRMZM2G168176_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 5
gtgatctatctcccatttttcagaatgaatttttatttggattaggttcattttttttgtgcaatgcaaagttcatgtcttagcaccatttgaattttagaaaccaacttattttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG
|| || |||    |  |||      | |||||| |||   | |           ||    |||||   ||||||      |||||   | ||||| |||       |   | |||| ||||||||||||||||||||||||||||| || ||||||||||| ||| |||| || ||||||||| |||||
gtaatatattagtctgtttgttttcttaattttcatt--aact---cctgccagttacaagcaata-gaagttc-----ctagcattgtctgaatattaccgtatgatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG
















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|101388447|gb|EB816210.1|EB816210
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTCCCCCACA-TGAGATTTGATAAAGT-GATAAAGGTGGTATGG
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCC-ACAATGAGATT-GATAAAGTTGATAAAGGTGGTATGG
EST: gi|148943696|gb|EC888763.2|EC888763
EST:     TATTTGTCTTCTCCATTGTGGATGGGCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTTCCCCACA-TGAGATTGATAAAGTTGATAAAGGTGGTATGGA
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTT-CCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGA
EST: gi|71325418|gb|DR799391.1|DR799391
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
EST: gi|71325419|gb|DR799392.1|DR799392
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGG
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGG
EST: gi|76283913|gb|DV023481.1|DV023481
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTTCCCACAATGAGATGGATAAAGTTGATAAAGGTGGTATGGAA
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
EST: gi|78180563|gb|DV550891.1|DV550891
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
EST: gi|18659405|gb|BM500320.1|BM500320
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
EST: gi|32945542|gb|CF050361.1|CF050361
EST:     TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT
genomic: TATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGAT

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), 49 (downstream exon)
Score: 83

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 53

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 50

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTATTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... attttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaagttcatgtcttagcaccatttgaattttagaaaccaacttattttgacagATTTCTGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG
                                          cttatttt  CT-rich tract
                      atttgaattttagaaa  TA-rich tract