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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatctatatctgtatcttttcatttcatatctcatcatccacgagtacaattattggttagtcctgacctacctagatgagttttctatcagatt...

Basic information

species Zea mays
transcript GRMZM2G007683_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007683_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g07760.1 (Oryza sativa), 5'ss of exon 2
GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatctatatctgtatcttttcatttcat-atctcatcatccacg--agtacaatt--attggttagtcc-tgacctacctagatgagttttctatcagatt
|||| | ||  |||||||||||||||| ||||| ||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||| ||   ||| ||||    || || |  |     |||||   ||||| | |   ||||||| | | ||| ||| | |    ||  ||||     |  
GGACAAGATTAGGAGGCCACTGATGCGGACGCGTGCCAATGATCCAGCCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATTGGCCTCCAAGTACCTgtgggtatctcta---gtacctttatgctttatcactttcctgtccacacaagtaccacttgtttggttaattcatgatctagcaatg-aaggattctgctgaa--
















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|211230003|gb|FL290138.1|FL290138
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227940|gb|FL290127.1|FL290127
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211230009|gb|FL290144.1|FL290144
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211230002|gb|FL290137.1|FL290137
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227943|gb|FL290130.1|FL290130
EST:     GGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAANGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCT
genomic: GGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAA-GTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCT
EST: gi|211227936|gb|FL290123.1|FL290123
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGARGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227938|gb|FL290125.1|FL290125
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATGGC
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATGGC
EST: gi|211227948|gb|FL290135.1|FL290135
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCG
EST: gi|211227945|gb|FL290132.1|FL290132
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGT
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGT
EST: gi|67027849|gb|CO456598.1|CO456598
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211230007|gb|FL290142.1|FL290142
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGA
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGA
EST: gi|211230006|gb|FL290141.1|FL290141
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTANCT                         ATTGATGTGTTGGAGGTCGATGGGGTC
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTC
EST: gi|211227941|gb|FL290128.1|FL290128
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227944|gb|FL290131.1|FL290131
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211230001|gb|FL290136.1|FL290136
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCG
EST: gi|60355379|gb|DN222352.1|DN222352
EST:     AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227935|gb|FL290122.1|FL290122
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         AATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagA-TTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227937|gb|FL290124.1|FL290124
EST:     GGTGCAAGAACTTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: GGTGCAAGAACT-CATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211230004|gb|FL290139.1|FL290139
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211230011|gb|FL290146.1|FL290146
EST:     GGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTAACCT                         ATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: GGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTA-CCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG
EST: gi|211227942|gb|FL290129.1|FL290129
EST:     AGGTGCAAGAACTCATGGGCAGTATCCGTGTCATCGGCCTCCAAGTACCT                         ATTGAKGTGTTGGAGGTCGATGGGGTCTATTATG
genomic: AGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG

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: 34 (upstream exon), 45 (downstream exon)
Score: 18

GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG


Block sizes: 34 (upstream exon), 45 (downstream exon)
Score: 56

GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 33

GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG


Block sizes: 34 (upstream exon), 46 (downstream exon)
Score: 31

GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatct ... actactgcagATTGATGTGTTGGAGGTCGATGGGGTCTATTATG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCAAATCCGGAGGCCACTGATGCGAACGCGGGCCAATGATCCAGTCAAGGTGCAAGAACTCATGGACAGTATCCGTGTCATCGGCCTCCAAGTACCTgtgggtatctatatctgtatcttttcatttcatatctcatcatccacgagtacaattattggttagtcctgacctacctagatgagttttctatcagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA