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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgcagtgaaatatatttttcctggatccgggcacttcaccaatggcacatttgtgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccgaatttaccattaatgcag

Basic information

species Zea mays
transcript GRMZM2G175510_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 7
CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgcagtgaaatatatttttcctggatccgggcacttcaccaatggcacatttgtgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccga-atttaccattaatgcag
||||||||||||| ||||| |||||| | ||||| |||||||||||||||||||  ||||| |||||||| ||||||| |   || ||   ||||                    ||   || ||| |||| |  ||| |    |   | |  |||   || ||| ||      |  ||||||| | |  || || |||||| |||||||
CATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACCgtaagtatat-gtcaagcttatta-------------------caaatattgcaaattt-tagtttggagaatctatgtatcgtcttctgtgtttt------tgttactgatttgagtgagatgtaccat-aatgcag

upper sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 8
CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgcagtgaaatatatttttcctggatccgggcacttcaccaatggcacatttgtgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccgaatttaccattaatgcag
||||  |||||||  | || |||||||||||||| ||||||||||||||||||||  |  |||   | ||||||||||||         |||   |    | |  ||    | |  |  ||    | |||  ||||        |         || |||  |  | | | || ||| |   |                          
CATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATCgtaagttt---------tattgctggtttagtacct--tattgtattaaaa--aaattcttgctcccaataataggaagaaagttcacagt-cgctgacaatttaaagcaagac-----------------------

upper sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G28650.1 (Glycine max), 5'ss of exon 8
CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgcagtgaaatatatttttcctggatccgggcacttcaccaatggcacatttgtgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccgaatttaccattaatgcag
|||| | ||||||  | || |||||||||||||| ||||||||||||||||||||  ||||||   | ||||||||||||              | || |||| |                | | || ||| ||  |||    |||| || | |    | || |    ||||| ||| ||| || |    |||   |   | | |    
CATATAACAAAGCTTTGGAGGATGCTATTGCTGTCCTTGACAAAATTGCAATGCCTATTGATGCTCAGGATCgtaagttt--------------tattgctggtt----------------tagtacctttttgtgttaaaaatttcttcctcccaatatta-ggaaaaaaaatttacactcatttt---gaagcaagactgagtc---

upper sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G35760.1 (Glycine max), 5'ss of exon 5
CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagttt-gcagtgaaatatatttttcctgg-atccgggcacttcaccaatggcacatttgtgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccgaatttaccattaatgcag
| ||   ||||||  | || ||||| |||||||| |||||||||||||| ||||| |||||||  ||||||||||||||| |  |  |  | | |||||| |   || |      ||    |   |  ||   | |    | || |||| | || | |    | ||    ||                                       
CTTATGACAAAGCTTTGGAGGATGCCATTGCTGTCCTTGACAAAATTGCTATGCCCGTTGATGCCAATGATCgtaagttttgttgctatttctctttttctttttattcttctcattttttaggagtgcaggagggtaacatccttttcttattccttatgatttgcagaaa---------------------------------------

upper sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 5'ss of exon 7
CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgcagtgaaatatatttttcctggatccgggcacttcaccaatggcacatttg-tgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccgaatttaccattaatgcag
||||||  ||||| || || |||||||||||||| |||||||||||||||||| |  | |||||||| || ||| ||||     || | || ||||   ||         || |    || ||  || ||||      ||        ||||| |   ||| |       ||| || |                                
CATACAATAAAGCTCTGGAGGATGCTATTGCTGTGCTTGACAAAATTGCAATGTCCATAGATGTGAAGGACCgtgagttcc---tggactacatttcctct---cttctacatt----cagtgttacgtttgacatgctaatttccctctctttcacacac-acacacacaaacataagcaca---------------------------

upper sequence: GRMZM2G175510_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 7
CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgcagtgaaatatatttttcctggatccgggcacttcaccaatggcacatttgtgctttagccctttcctcttgcgtgcactatgtgttaaaaaattatactgatgtcaccgaatttaccattaatgcag
| || |  ||||| ||||| ||||||||||| || |||||||| ||||||   || |||||||||||||| |||||| ||  |    ||||| |   | ||   |    |||||||           ||||| | |  |     |   | | | ||  | | |    |    ||||| |   |                          
CTTATAATAAAGCTCTTGAGGATGCTATTGCGGTGCTTGACAAGATTGCAGCCCCTGTTGATGTGAATGACCgtaagcttttac---aatatttcccttcttattttatgcacttctttt------tatttgagttaaaatttctctttgtagtgtttatt-tac-ctgggtaattagaaata--------------------------

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|71438455|gb|DR819505.1|DR819505
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|211175329|gb|FL101110.1|FL101110
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCCAT-GGTACAAA-TTCACT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCC-ATTGGTACAAAATTCACT
EST: gi|211175332|gb|FL101113.1|FL101113
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCTGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|211175327|gb|FL101108.1|FL101108
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGT
EST: gi|71332448|gb|DR803183.1|DR803183
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|31360791|gb|CD445148.1|CD445148
EST:     CAAAATTGCAATGCCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: CAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|31354620|gb|CD438977.1|CD438977
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|211175325|gb|FL101106.1|FL101106
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGT
EST: gi|211175333|gb|FL101114.1|FL101114
EST:     TGCTATTGCTGTACTTGACNAAATTGCAATGCCTGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAA-TTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|71428865|gb|DR809915.1|DR809915
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|94478012|gb|EB706970.1|EB706970
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|71448421|gb|DR829471.1|DR829471
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
EST: gi|211175328|gb|FL101109.1|FL101109
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCTGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCA
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCA
EST: gi|30306946|gb|CD001619.1|CD001619
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCT
EST: gi|74244741|gb|DT652655.1|DT652655
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC                         GCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTG

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: 158

CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 88

CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

CATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATCgtaagtttgc ... attaatgcagGCGGGGCAATGCTAGGCCTCGTGAAGAGCTCCATTGGTACAAAATTCACTGGCCAGTTTGGTGATCTTATTGCT