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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctttttgccaaatagtgtgtttttcatttcctttcaatacactggccttactttgccctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT

Basic information

species Zea mays
transcript GRMZM2G116086_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 9
gtttctttttgccaaatagtgtgtttt--tcat-ttcctttcaa---tacactggccttac--tttgccctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT
|||  |||||  |  ||    | ||||  | || ||  || |||   | | |     |||   | |||| | |  | ||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| 
gttaatttttatctgatgactttttttggttatattttttgcaactttcctccatatttatcatctgccttcttttggacagGGGTACAATAAGATATGCTAGTGTCCATGCCCATTTAGGCCGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTAATATTTCTTCTC

upper sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttcttt-ttgccaaatagtgtgtttttcatttcctttca---atacactggccttac---tttgc--cctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT
|| | ||  |||    ||  | | |||   | |    ||     ||| | |   || ||   ||||   |  ||| |   |||||| |||||||| || || |||  |||||||||| | || ||||| || ||  | |||||||||||||| ||||| || |||||||| ||||||||  | 
gtattttgattggtgtatgttatctttcctactattgttggtatatatattttgctcacatctttgttacgcttcatatgcagAGGAACAATAAGGTATGCAAGTTGCCATGCACATCTTGGTCGTACAGGAAGTCGGAGGGATGATCTGGAGTCATTGGCTTATACATTAATATTTCTGATG

upper sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 9
--------gtttctttttgccaaatagtgtgtttttcatttcctttcaatacactggccttactttgccctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT
         |||||   ||   | ||           |  | |||| |      |    | | |   | | |   ||| ||| || |||||| | || || ||||| ||||||||||||||||| || || || |||||||||||||| || ||| |||| || ||||| ||||||||  ||
gtttgtggatttctggatgttca-taaaaaaaaaaaaaaatgctttgacctttataatat-attaatctcctcttttggcagGGGAACAATACGGTATGCAAGTGTGCATGCACATTTAGGACGGACAGGAAGTAGAAGGGATGATCTCGAGTCACTAGCTTACACATTAATATTTCTCATT

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|22935976|gb|BU572251.1|BU572251
EST:     GGGTCATCTGGACAACATGCTGAATATGATCAGAAACCAGATATTTTCAG                         AGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
genomic: GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
EST: gi|67028330|gb|CO457079.1|CO457079
EST:     GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG                         AGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
genomic: GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
EST: gi|6865205|gb|AW360555.1|AW360555
EST:     GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG                         AGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
genomic: GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
EST: gi|87155883|gb|DY400672.1|DY400672
EST:     GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG                         AGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
genomic: GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
EST: gi|26559656|gb|CA831891.1|CA831891
EST:     GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAG                         AGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG
genomic: GGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAG

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), 49 (downstream exon)
Score: 228

CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT


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

CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 262

CATCTAGATGGAAGGAATCAGGGTCATCTGGACAACATGTTGAATATGATCAGAAACCAGATATTTTCAGgtttcttttt ... tccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtttttcatttcctttcaatacactggccttactttgccctttccttgacagAGGTACAATAAGATACGCTAGTGTCCATGCACATTTAGGACGTACTGGTAGCAGAAGGGATGATCTGGAATCATTAGCATATACATTGATATTTCTTCTT
                             gccttac  putative branch site (score: 262)
                              ccttactttgcccttt  CT-rich tract
     ttttcattt  TA-rich tract