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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC

Basic information

species Zea mays
transcript GRMZM2G470556_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 9
gtaagaattcattcttgt---catttgaagcatgaatcgtagttacactcactaatt-tctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
||||||| | | ||  ||   | ||  ||  |  |    |  || ||  ||  |||  |  |  | ||| |||||||| ||||||| | |||||||| || |||||||||| |||||||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| | |||||||||||| |
gtaagaaattagtccagtattctttcaaaagaacaccaatcatttcaagcataaatcatacgtgaaactgttttttatcaaatgtttggcagGCTGTCCTTTTGTTCCAGAAAATAGAAGGTGTAGAAGTGTGCCTATTTGGAATGTATGTTCAAGAATTTGGTGCAGAATGCTCCTACCCGAACCAGCGTC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 11
---gtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaat-ttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
    | ||||       || ||| |   | | | ||||| |     | |||  ||| || |   |  |  ||   | |  | |      ||||  ||| | ||||| || |  ||||||||||||||||| || |||||||||||||||||||||||||||||  | |||||    |  || || |||||||
gtgatgagaaagttgatttatcaatctgatcgt-aatcgaatcattaatcatgaatattatttgatgcccttagctttctattc-----cagGTAGTTTTGTTGTTTCAAAAGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 9
------gtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
      | |||  | | ||   |  | |         ||||  |||     | | | ||| ||| |     ||   || ||   |      ||||   |  | ||||| ||||  || ||||||||||||||||| || |||||||||||||||||||| |||||  | |||||    |  ||||| || || |
gtaaagggaaggttgctttagagctagtcatgttggtaatca-agtcgttattatttatt-ctggattttgatgacttttggtttccatttcagGTAATCTTGTTGTTTCAGAAGATTGAAGGTGTGGAAGTATGCCTCTTTGGCATGTATGTTCAAGAGTTTGGATCTGAATGTCAATTTCCGAATCAACGGC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 9
-----gtaagaattcattcttgtcatttgaagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
     |  | | || ||| |   |||  ||      ||||  |     | |||  |||   |   |  |  ||   | |  | |      ||||  ||| | ||||| || || ||||||||||||||||| || |||||||||||||||||||||||||||||  | |||||    |  || || |||||||
gtgatgggaaagttgattttatccatccga--ttgtaatcaaatcattaatcatgaatacttttgattcccttagctttctattc-----cagGTAGTTTTGTTGTTTCAAAGGATAGAAGGTGTGGAAGTTTGCCTATTTGGCATGTATGTTCAAGAATTTGGATCTGAATGTCAATTTCCTAATCAGCGCC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------gtaagaattcattcttgtcatttg--aagcatgaatcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
                           |     ||| ||||| |  |||   ||  ||||      | |||| | |    | |   | |     ||   ||   | | ||   |||||  |||| ||||| ||||  || |||||||| ||||||||  |||||||||||||||| || ||||||||  |||| |   | || || || |||||||
gtacagattgtgtatgcttggttcttatttcttttccttctttttgttttctaattatgaccttctgctaca-tgatgcctgttgactatcaacttccatactcattttttttcagGCCATTCTGTTGTTTCAGAAGATTGAAGGTGTTGAAGTATGCTTATTTGGCATGTATGTCCAGGAATTTGGAACAGATTCTGCGTCTCCCAATCAGCGCC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------gtaagaattcattcttgtcatttgaagcatgaatc--gtagttacactcactaatttctgcaacactattttttatg----aaatgttg---gacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
               | |     ||||| |  |   || | |     ||    || || ||         |  || |  | |||  ||  ||    | || ||      ||||  |||||  |||||||||  ||||||||||| ||||||||  | ||||| |||||||| |||||||||||  | ||||| ||    || || || ||||
gtaagaatgatcgacgcacaccatcattgtatttgcttcatgtccacatttaatattttcaggattcctctcttgtagtaatatcgttcgtgctccacattttatttatcagGTGGTTCTGCTGTTCCAGAAGATAGAAGGTGTAGAAGTATGCTTGTTTGGGATGTATGTCCAAGAATTTGGATCCGAATGTTCAAATCCCAATCAACGCC

upper sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaattcattcttgtcatttgaagcatgaat-cgtagtt-acactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
||| | |     | |  | | |||| |  |       ||||| |||   ||| |  |    |||   |  || | |     |||   ||||   || | ||||| ||||  || ||||| || ||||||||  ||||||| ||||||||||||||||||||  |||||||    | ||| || || || |
gtatgcaggatgtatattaagttgatgttttttcatatagttgacaaagacttaaattatgaactgaagattgtctttttcgtttc-cagGTAATTTTGTTGTTTCAGAAGATTGAAGGAGTAGAAGTATGCTTATTTGGGATGTATGTTCAAGAATTTGGATCAGAATGTCTATTCCCAAATCAACGTC

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|211057050|gb|FL391369.1|FL391369
EST:     AATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGG
genomic: AATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAA-GTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGG
EST: gi|211363258|gb|FL387051.1|FL387051
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211299426|gb|FL430297.1|FL430297
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211235994|gb|FL378061.1|FL378061
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAAGGTGTGGAAGTATGTCTATTTGG
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAG-AAGGTGTGGAAGTATGTCTATTTGG
EST: gi|211299429|gb|FL430300.1|FL430300
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGGTCTCTTGTTCC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCC
EST: gi|211022186|gb|FL381963.1|FL381963
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATANAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211490473|gb|FL383680.1|FL383680
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211539239|gb|FL396300.1|FL396300
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211179796|gb|FL384668.1|FL384668
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATANAAGGNGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211153694|gb|FL418631.1|FL418631
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211085796|gb|FL424018.1|FL424018
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGNGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211046001|gb|FL422502.1|FL422502
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211343346|gb|FL378210.1|FL378210
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
EST: gi|211398119|gb|FL400636.1|FL400636
EST:     AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAG                         GCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC
genomic: AAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGC

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: 37 (upstream exon), 49 (downstream exon)
Score: 57

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 49

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 61

AGTTGTTTCATCAGTGGATAAAAAGCTGGAGGTTAAACCACGTTTTTTGGAAATTTTTCAAGAAGACAACTACCCTACAGAGTTCCCTTACAAGTCCAAGgtaagaattc ... tgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtagttacactcactaatttctgcaacactattttttatgaaatgttggacagGCTGTTCTCTTGTTCCAGAGAATAGAAGGTGTGGAAGTATGTCTATTTGGCATGTATGTTCAAGAATTTGGTGCAGAATGCTCTTCCCCGAACCAGCGCC
             cactaat  putative branch site (score: 61)
                               tattttttatgaaatg  TA-rich tract