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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatctgaactttaacttgttctacattgcagttatactactgcccaagtgacattttgaagtattaatcaatgcatactagtgtagtcacaaaaa...

Basic information

species Zea mays
transcript GRMZM2G337532_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337532_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os04g52590.1 (Oryza sativa), 5'ss of exon 14
TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatctgaactttaactt------gttctacattgcagttatacta-ctgccca-agtgacattttgaagtattaatcaatgcatactagtgtagtcacaaaaa
||||||||||||||||||||||||||||||||||| ||||| ||||||||| || | || |||||||| |||||||||||||| |||| || |||||||||||| |||| |||| || || |||||| ||| | ||||||||| ||| || | | ||||| | ||| | || ||| || ||
TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGTACTTGCTGCATTCCTCATCAAGGCTACTATGGGCCTGCAATATCAGCTTTGAGCGCTACTCCAAgtactgatctaaactagaattttttttcgttctatatttctgttatactaactgttcacaacgccatttgggagt--catctaagatatatcggtatacctc------

upper sequence: GRMZM2G337532_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G25590.1 (Glycine max), 5'ss of exon 20
TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatctgaa------ctttaacttg--ttctacattgcagttatactactgcccaagtgacattttgaagtat-taatcaa----tgcatactagtgtagtcacaaaaa------------------
| ||||||||||||||||| |||||||| || || ||||||||||| || | | || ||||| || ||| ||| | ||| | |||| ||| | | |||| ||| || | | ||| | | | | || | || | | || || |||| | ||| | | || | | | |
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATTCCAGgtaatactatgaaaaaaattggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatttttttaatttgatacattgttttgtgttgtacag

upper sequence: GRMZM2G337532_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G25600.1 (Glycine max), 5'ss of exon 17
TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatctgaactttaacttgttctacattgcagttatactactgcccaagtgacattttgaagtattaatcaa-tgcatactagtgtagtcacaaaaa----------------------------------
| ||||||||||||||||| |||||||| || || ||||||||||| || | | || ||||| || ||| ||| | ||| | ||| ||| | | |||| || ||| | | | | ||| | |||| || || || | |||| | ||| | | | | | | |
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATCCCAGgtaatactatgaaaaa-aatttggta-atttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattca-aaatttatatatatttttaatttgataaattgttttgtgttgtacag

upper sequence: GRMZM2G337532_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv00s0125g00210.t01 (Vitis vinifera), 5'ss of exon 2
TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgta-ctcatctgaactttaactt---gttctacattgcagttatactactgcccaagtgacattttg--aagtattaatcaat-gcatactagtgtagtcacaaaaa
| ||||| |||||||| ||||||||||| ||||| ||||| ||||| |||||| | || || ||||| || | || |||||||| |||| | || ||| | ||| | || || | | | || | | ||| | ||||| || | | | ||| | | || | || | |
TATCTTGAAATTCATCTGTTCTGGGCTGGTAAGGGAACTTGCTGCATACCTTATGATGGTTATTATGGACCATCCATTTCAGCCCTCAGTGTTGTTTCAGgtaacccatttaaatgatagttatagaattcatataatataagatgtcctgactggtgcttcttttgccaactgcaactgaattggttgctgatttattttgctcag

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|160481411|gb|EY254305.1|EY254305
EST:     TTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAA                         ATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAA
genomic: TTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatct ... tcttcttcagATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAA
EST: gi|32837254|gb|CD976932.1|CD976932
EST:     TCAGCCCTGAGTGCAACTCCAA                         ATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAA
genomic: TCAGCCCTGAGTGCAACTCCAAgtactcatct ... tcttcttcagATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAA

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: 68

TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatct ... tcttcttcagATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAACTGGTGTGATCGCTGGGGTTGCAGTTGGTGTTTCAGTTTTTGCATTGAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 82

TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatct ... tcttcttcagATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAACTGGTGTGATCGCTGGGGTTGCAGTTGGTGTTTCAGTTTTTGCATTGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 153

TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatct ... tcttcttcagATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAACTGGTGTGATCGCTGGGGTTGCAGTTGGTGTTTCAGTTTTTGCATTGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

TTCCTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTTATAAGGGATACTATGGTCCTGCAATATCAGCCCTGAGTGCAACTCCAAgtactcatct ... tcttcttcagATTTCGTTCCTACAGTCCGTAGTTCTGAAGACAGCAAGAGCAGCCATAAAACTGGTGTGATCGCTGGGGTTGCAGTTGGTGTTTCAGTTTTTGCATTGAT