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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacaggctgcacatgtctgatctacattttgagcctttcctgtaggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG

Basic information

species Zea mays
transcript GRMZM2G158627_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 3'ss of exon 24
---------------------------------------------------------------------------------------caacaggctgcacatg-tctgatctacattttgagcctttcctgtaggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG
                                                                                       || || | |  |     | | |||  ||      |   ||       | | | |  |  |  |        || |     | ||    ||| | || |||||||||  |  | |||||||||||||||||||| |||||||| |||||||| | ||||||||||    | ||  |  |  ||   ||||| |||   ||||
gtgagtttggatattctccctgtttcagtttactgttaactgacttttatctctatcaattggaggatttgatttttcttacatgaacaccaagttatatgcactatcatcaccaccaattggtgttgacacgagttgaaatggatataaaacatttaatctcattgtcatttgtctggt-ttggcagGTAATGATCTGTGAGGAGTCTCACAATGTACAAGACATGTCGTTTGTCATTTACATTGCAAGGGTTTCTCCAGTGGTCACAGATGATCTCCTTGTCCATG
















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|71432888|gb|DR813938.1|DR813938
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|40334151|gb|CK368221.1|CK368221
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|60345148|gb|DN212121.1|DN212121
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|78022271|gb|DV490658.1|DV490658
EST:     ACGCACTTGGTTCGCCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|45568479|gb|CK986083.1|CK986083
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|166516458|gb|EG268171.1|EG268171
EST:     AATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTG-CATA
genomic: AATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|113702485|gb|EE679989.1|EE679989
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTATTACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|211108629|gb|FL325826.1|FL325826
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|37373885|gb|CF623267.1|CF623267
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
EST: gi|60337676|gb|DN204649.1|DN204649
EST:     ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGAT                         GTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA
genomic: ACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATA

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), 47 (downstream exon)
Score: 120

TATATTAGGGACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TATATTAGGGACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 72

TATATTAGGGACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 59

TATATTAGGGACGCACTTGGTTCACCAATTATGCCAAAAGAAATGGCACCAACAGATGATgtaagtttcg ... ttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcacagaggcaatatgggcaatatttagagtttatcaaactgttgtttgcagGTAATACTTGGCGAGGAGTCTCACAATGTACATGACATGTCATTTGTCATATGCATTGCAAGGTCCACCCCTATTCTTGCACCAGATCTTCTTTCTCATG
                      aatatttagagtttat  TA-rich tract