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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcaccattcggtgcaacaccttgtgcgcttagagacatgtagcaacgtatgtataaagacggctgattctgttcctgatgttgtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT

Basic information

species Zea mays
transcript GRMZM5G835323_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835323_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g34589.2 (Oryza sativa), 3'ss of exon 4
gtacgcaccattcg----gtgcaacaccttgtgcgcttaga----gacatgtagcaacgtatgtata-aagacggctgattctgttcctg-atgttgt-cctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT--
||| | | |||||     |||||   | |  |||  |||||     |||||  |  | ||||| | | || ||| ||     ||||     ||| | |  |  |||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||    |||| |||||   ||  |   |   ||   ||  || |   |  
gtagggatcattcttcttgtgca-tgcttactgcaattagatgtacacatgctgtgatgtatgaaaagaatacgtcttgacttgttgtaacatgctatgtcccgcagGCCGGCATTGTGAAGAAGGAACACATCAAGATTCATGGTTTCTGAGCAACTGCCAAAACCATTGCAAA--GACTATAGTTTGGGGTGGAGTATACTTGGTTG

upper sequence: GRMZM5G835323_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv19s0177g00100.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtacgcaccattcggtgcaacaccttgtgcgcttagagacatgtagcaacgtatgtataaagacggctgattctgttcctgatgttgtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCG---GGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT
                      |||||    |   | |         |  | | | ||  |   | | |   | |||      || ||  |||  ||   |        ||||| |||||||||||||||||| | |||||||||||||||||||||    | || |   | |   |  ||  | ||  ||  || |     | |  ||||| | 
gtaatgtgatgtttctccctttaccatcaactttgaaaatcaaaaatcaaatacatatccattcaagcacaaacaaattgatgtggtttggttattggcttccctgcaacagGCTGGCATTGTGAAGAAGGAGGATATCAAGATTCATGGTTTCTGATTTGCTGCGGATCGATTTCTGACAGGCGAATGCT--ATCCCCTATCCGGATATTAGA-
















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|166628457|gb|EG158109.1|EG158109
EST:     GGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAAGCAAC
genomic: GGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGA-GCAAC
EST: gi|83279159|gb|DV943167.1|DV943167
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTTTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|21621225|gb|BQ619231.1|BQ619231
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|71767976|gb|DR965913.1|DR965913
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|50332863|gb|CO527989.1|CO527989
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|60356711|gb|DN223684.1|DN223684
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|33092763|gb|CF052757.1|CF052757
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCTTCTTTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|211485134|gb|FL401515.1|FL401515
EST:     TCAGCTCCCAGG-TGATCAGAAGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCANGATTCATGGTTTCTGAGCA
genomic: TCAGCTCC-AGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCA
EST: gi|4730501|gb|AI649667.1|AI649667
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|71441941|gb|DR822991.1|DR822991
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|211116916|gb|FL407738.1|FL407738
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|28576067|gb|CB281959.1|CB281959
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCCCATCAAGATTCATGGTTTTTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|78080734|gb|DV509146.1|DV509146
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|32865911|gb|CF005593.1|CF005593
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAAAAGGAGCCCATCAAGATTCATGGTTTTTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|40303767|gb|CK348154.1|CK348154
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|113701876|gb|EE679380.1|EE679380
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCTTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|5510841|gb|AI857225.1|AI857225
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|91871868|gb|EB401825.1|EB401825
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|71761988|gb|DR959925.1|DR959925
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|4610125|gb|AI600964.1|AI600964
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTTTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|78112906|gb|DV531300.1|DV531300
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|166623445|gb|EG143889.1|EG143889
EST:     TGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|14204119|gb|BG837796.1|BG837796
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|87155007|gb|DY399796.1|DY399796
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCTTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTTTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|113660296|gb|DW818607.1|DW818607
EST:     GAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: GAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|113702845|gb|EE680349.1|EE680349
EST:     TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
EST: gi|60395875|gb|DN228745.1|DN228745
EST:     ----GCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAG                         GCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC
genomic: TTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACC

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: 799

GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2731

GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2921

GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1454

GCTGCCCGCTATAGGTCATTCAGCTCCAGGGTGATCAGAGGAAGAACGTCTCGAATTTCCTCGTCCAGgtacgcacca ... gtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagcaacgtatgtataaagacggctgattctgttcctgatgttgtcctggcagGCCGGCATTGTGAAGAAGGAGCACATCAAGATTCATGGTTTCTGAGCAACCGCCGGGTCCATAGCAAACCAACCCTGCATGCAGGGCCAGCTTATTATAT
                                   tcctgat  putative branch site (score: 1454)
                                           ttgtcct  CT-rich tract
          tatgtataaa  TA-rich tract