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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagagttaattattatgttggttcctgtgaatgcatagggaccatgttaagtaagttgttatttagttctgacaaatataaattggcaaacttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT

Basic information

species Zea mays
transcript GRMZM2G471805_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G471805_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g57330.2 (Oryza sativa), 3'ss of exon 4
aagagttaattat-tatgttggttcctgtgaatgcatagggaccatgttaagtaagttgttatt--tagttctgacaaatataaattggcaaacttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT
 | | | | |  |   |  |||||  | | | |   | |           |  || | |   ||  |||||||   ||  ||  |||   |      ||||||   ||||||||||  | || |||||||||||||||||||| |||||||| ||||| |  || ||||| |||||||| |||||||| ||||||||||| ||
-acaataagtggtgcctagtggttagt-taagtttgtggaagtttctcataacaattggacgttgctagttctcctaacaattgattt-tacgtggcaaacagGCTCCATCGGCTCTGTCACCGTTGCAGAATTGGACTGGGGTAACAAAGATCATATAAGAGCTGTTGATCCTCCATTCGATTACATCATTGGAACTGATGT
















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|211397545|gb|FL373943.1|FL373943
EST:     AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAG                         ATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
genomic: AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
EST: gi|211243538|gb|FL421850.1|FL421850
EST:     AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAG                         ATACCATCGGACTCAATTACAGTTGCAGAATTGGACTGGGGGAACAA
genomic: AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGG-CTCAATTACAGTTGCAGAATTGGACTGGGGGAACAA
EST: gi|211341427|gb|FL403611.1|FL403611
EST:     AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAG                         ATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
genomic: AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
EST: gi|60395803|gb|DN228673.1|DN228673
EST:     AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAG                         ATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
genomic: AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
EST: gi|211019758|gb|FL395380.1|FL395380
EST:     AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAG                         ATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC
genomic: AAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAAC

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: 46 (upstream exon), 48 (downstream exon)
Score: 31

TGTGATGTTACAACAACTGACCAAGTCGAGGTGCTTCCGCTGCTTATGAGAAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 16

TGTGATGTTACAACAACTGACCAAGTCGAGGTGCTTCCGCTGCTTATGAGAAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT


Block sizes: 45 (upstream exon), 35 (downstream exon)
Score: 6

TGTGATGTTACAACAACTGACCAAGTCGAGGTGCTTCCGCTGCTTATGAGAAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT


Block sizes: 32 (upstream exon), 48 (downstream exon)
Score: 20

TGTGATGTTACAACAACTGACCAAGTCGAGGTGCTTCCGCTGCTTATGAGAAATGTTGAACGCAACAGATCTTGGATTTCGCAATCGAATTCCGACACAGgttttgtgga ... cttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaagtaagttgttatttagttctgacaaatataaattggcaaacttaaaacagATACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGT
                     ttctgac  putative branch site (score: 20)
                        tgacaaatataaatt  TA-rich tract