Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctatctctccatttgtcagattgaatttttgtttggattaggttcatttttgtgtgtgcgcaatgcaaacatcatgtcttagcaccattgaattttagaaacctaatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG

Basic information

species Zea mays
transcript GRMZM2G160458_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 5
gtgatctatctctccatttgtcagattgaatttttgtttggattaggttcatttttgtgtgtgcgcaatgcaaacatcatgtcttagcaccattgaattttagaaacctaatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG
|| || |||   ||  |||||    || |  ||||  ||   |   |    ||        |      | | | |||  ||||| |  |  |  | ||       | | | |||| |||||||| |||||||||||||||||||| || ||||||||||| |||||||| || ||||||||| |||||
gtaatatattagtctgtttgttttcttaa--ttttcattaactcctgccagttacaagcaatagaagttcctagcat--tgtctgaatattaccgtat------gatcaactttgtcagATTTCTGTTCCCCACAATGAGATTGACAAGGTTGATAAAGGAGGTCTGGACAAGATGACACTTGTTGAG
















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|110202290|gb|EC884187.1|EC884187
EST:     GTTTTGTCTTTTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCCCAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: G-TTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|71429209|gb|DR810259.1|DR810259
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTG
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTG
EST: gi|148946148|gb|EC891442.2|EC891442
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|148946147|gb|EC891441.2|EC891441
EST:     TGTTTGTTTTTTCCATTGTGGATGGCCATGTTTGGTTTGGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|148996317|gb|EE035601.2|EE035601
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTTGATAA-GGTGGTCTGGA
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTT-GATAAAGGTGGTCTGGA
EST: gi|149070865|gb|EE159274.2|EE159274
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|50323762|gb|CO518888.1|CO518888
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAA
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAA
EST: gi|110196089|gb|EC877986.1|EC877986
EST:     TGTTTGTTTTTTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCCCAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|33468119|gb|CF245168.1|CF245168
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCGCAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|71429925|gb|DR810975.1|DR810975
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|71301915|gb|DR787034.1|DR787034
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|211114336|gb|FL479348.1|FL479348
EST:     TGTTTGWCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTC-GTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|60347622|gb|DN214595.1|DN214595
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|71429926|gb|DR810976.1|DR810976
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCAGGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGA
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGA
EST: gi|78089923|gb|DV518297.1|DV518297
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
EST: gi|71426064|gb|DR807114.1|DR807114
EST:     TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCCACA-TGAGATTG
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCC-ACAATGAGATTG
EST: gi|86469691|gb|DY236061.1|DY236061
EST:     TGTTTGTTTTTTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAG                         ATTTCGGTTCCCCCCAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT
genomic: TGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGAT

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), 46 (downstream exon)
Score: 208

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG


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

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 38

ATTTGCTACTCCTAAAGATCACCGTAAAGCAAAACCTTTCCATGACCATGTGTTTGTCTTCTCCATTGTGGATGGCCATGTTTGGTTTCGAAACTACCAGgtgatctatc ... aatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatgcaaacatcatgtcttagcaccattgaattttagaaacctaatttggcagATTTCGGTTCCCCACAATGAGATTGATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG
                                         acctaat  putative branch site (score: 38)
                           attgaattttagaaa  TA-rich tract