Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctcttcctcctccccctcctgcttgctcaatctcgctccggtcacgaattgcttgtgccccccaattccgttgactgacatgtgtttcgaccgtgcgcacgttgcag

Basic information

species Zea mays
transcript GRMZM2G171073_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171073_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g10140.1 (Oryza sativa), 5'ss of exon 2
AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctcttcctcctccccctcctgcttgctcaatctcgctccggtcacgaattgcttgtgccccccaattccgttgactgacatgtgtttcgaccgtgcgcacgttgcag
|||||||||||||||||||||| ||||| |||||||||||||||  ||||||||||||||||||||||||||||||||| ||||||||| | ||||| ||||||||| ||   |||    |||  |   |  | ||  |||    ||  ||      | |  || ||  | | || |  | |   ||                           
AGTGCTCCAAGAAGTACGCCGTCCAGTCCGACTGGAAGGCGCACACCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGACTGCGGCACCTTATTCTCACGgtccgtcttccctctcgattcccatccaatctc-catcctctaatcgagcagccgccgatactgaccggcgaatc-gccgccgcgcag--------------------------

upper sequence: GRMZM2G171073_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G06500.1 (Glycine max), 5'ss of exon 2
AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctcttcctcctccccctcctgcttgctcaatctcgctccggtcacgaattgctt-gtgccccccaattccgttgactgacatgtgtttcgaccgtgcgcacgttgcag
||||||||||||||||||| || ||||| || ||||||||||||   ||   ||||||| |  | |||||    ||||| ||||| ||| | |||||| ||| |||   | |    ||| |   | || |||   ||| |  ||   ||   |  | |||     |     ||  || |||  ||     ||||  ||      |          
AGTGCTCCAAGAAGTACGCGGTTCAGTCCGATTGGAAGGCGCACTCTAAAGTCTGCGGCACAAGAGAGTATAAGTGCGACTGCGGAACCGTTTTCTCCAGgttcgtttccctttctctctcttgcttgattgtctaattt--cttttgttttgtttcgctccactctaaaaaaagcctttgcttggt---tgttgggatttgaag----------

upper sequence: GRMZM2G171073_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G25550.1 (Glycine max), 5'ss of exon 2
AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctcttcctcctccccctcctgcttgctcaatctcgctccggtcacgaattgct-tgtgccccccaattccgttgactgacatgtgtttcgaccgtgcgcacgttgcag
||||||||||||||||||| || ||||| || ||||||||||||  |||   ||||||| || | |||||    ||||| || || ||| | |||||| ||| |    | ||  |  |    ||    ||  ||   | | | ||   |   |  ||| | |||    | |   |||  |  || |    |  || |   ||  | |  ||| ||
AGTGCTCCAAGAAGTACGCTGTTCAGTCCGATTGGAAGGCGCACTCCAAAGTCTGCGGCACCAGAGAGTATAAGTGCGACTGTGGAACCGTTTTCTCCAGgttcccttttttttttttttttctttctctctcttggttttg-tctaatt-tgttttgttctgttttactccgctccact--ctaaaggcttgtttggttgttgggat-ttgaag

upper sequence: GRMZM2G171073_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0001g12220.t01 (Vitis vinifera), 5'ss of exon 2
AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctcttcctcctccccctcctgcttgctcaatctcgctccggtcacgaattgcttgtgccccccaattccgttgactgacatgtgtttcgaccgtgcgcacgttgcag
 ||||||||||||||||||||||||||| || |||||||||||  | || || |||||  || | || |||   ||||||||||| ||  | || ||  ||| |    || |     ||  |    | | |  |  |  ||    | |  | |   ||||  |   ||            | | | | |   |   |  ||   ||        
GGTGCTCCAAGAAGTACGCCGTGCAGTCAGATTGGAAGGCGCATTTGAAAACTTGCGGTACCAGAGAATACAAATGCGATTGCGGAACTTTGTTTTCGAGgttctctatcgtttctttcttctcatttccttttacacttcttctccgcta-ggtctgctgataatcctggga------aattaaaaagaaatggaaaagtttacaa-------

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|91051718|gb|EB162136.1|EB162136
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTG
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTG
EST: gi|149079811|gb|EE168809.2|EE168809
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|149004453|gb|EE039076.2|EE039076
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCTCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|78106463|gb|DV524881.1|DV524881
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|78109193|gb|DV527610.1|DV527610
EST:     CCTGCGGCTCCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCCTCCACCCCCCGCGCCTTCTGTGACGCGCTTGCCGAAG
genomic: CCTGCGGCTCCC-GCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATC-ACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAG
EST: gi|71439765|gb|DR820815.1|DR820815
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|148973264|gb|EE024343.2|EE024343
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|148989685|gb|EE031768.2|EE031768
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|76913956|gb|DV165339.1|DV165339
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTG
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTG
EST: gi|78112595|gb|DV530989.1|DV530989
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCC                         GAGGGACAGCTTCATCACCCACCGCGCC
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCC
EST: gi|76014993|gb|DT942163.1|DT942163
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|76015015|gb|DT942185.1|DT942185
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|71313169|gb|DR793116.1|DR793116
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|149037291|gb|EE155335.2|EE155335
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCTCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCT
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCT
EST: gi|71437227|gb|DR818277.1|DR818277
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCGCCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGC
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGC
EST: gi|149098029|gb|EE183976.2|EE183976
EST:     CCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCCTCT-CTCCCG                         GAGGGACAGCTTCATCACCCCAC-GCGCCT
genomic: CCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCC-TCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCC-ACCGCGCCT
EST: gi|74243979|gb|DT651893.1|DT651893
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|71323979|gb|DR798675.1|DR798675
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGA
EST: gi|71444559|gb|DR825609.1|DR825609
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTTGC-GAAA
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTT-GCCGAAG
EST: gi|148945429|gb|EC890660.2|EC890660
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCC
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCC
EST: gi|71437740|gb|DR818790.1|DR818790
EST:     ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCG                         GAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCG
genomic: ACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCG

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), 42 (downstream exon)
Score: 73

AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGAGAGCGCCAAGGCGCGGGCGGAGGCGCCTTCCGCGGAGGATGGGAGCTCG


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 16

AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGAGAGCGCCAAGGCGCGGGCGGAGGCGCCTTCCGCGGAGGATGGGAGCTCG


Block sizes: 41 (upstream exon), 43 (downstream exon)
Score: 18

AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGAGAGCGCCAAGGCGCGGGCGGAGGCGCCTTCCGCGGAGGATGGGAGCTCG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 10

AGTGCTCCAAGAAGTACGCCGTGCAGTCGGACTGGAAGGCGCACGTCAAGACCTGCGGCTCCCGCGAGTACCGCTGCGATTGCGGCACCCTCTTCTCCCGgtccgtcctc ... cacgttgcagGAGGGACAGCTTCATCACCCACCGCGCCTTCTGTGACGCGCTTGCCGAAGAGAGCGCCAAGGCGCGGGCGGAGGCGCCTTCCGCGGAGGATGGGAGCTCG