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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaacattttatgacttaactcttattgatgcatgctcaaatgctcacttgtgcaaacaagtagcatttttgtgctttgcgtgtgaagtttgttta...

Basic information

species Zea mays
transcript GRMZM2G050961_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050961_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv15s0021g00830.t01 (Vitis vinifera), 5'ss of exon 5
ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaacattttatgacttaactcttattgatg--catgctcaaatgctcacttgtgcaaacaagtagcatttttgtgctttgcgtgtgaagtttgttta---------------------------------------------------------------------------------------------
||||| || || |||||||| ||  | ||||||||||||||||||||||||| |||   |    ||  |   | || ||| ||  | ||   ||||  |   ||  |  ||  | |   |||  ||    | |     |    || |  |                                                                                             
ATTCTCTCTATTGGTGCTGATGTTGGGGAAGTTGAGGCTGGGAAGAAGgtaatgaatcataatggatcttctttttgttggtgttcttgtataaataattttttcagtgaattatttatattgatgccactgggactagtgaattctccaagaagctggactttctatgcgcttaatggcattttttttatattctagtgcttttataccatctaaaggaagggaatggctatctttttgcag
















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|13558469|gb|BG549825.1|BG549825
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|148943634|gb|EC888698.2|EC888698
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|211482968|gb|FK973427.1|FK973427
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGNTGGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTA
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGG-AAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTA
EST: gi|15198996|gb|BI423600.1|BI423600
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|148943633|gb|EC888697.2|EC888697
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|166466537|gb|EG225135.1|EG225135
EST:     AGATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: AGATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29577011|gb|CB617123.1|CB617123
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|19058136|gb|BM736803.1|BM736803
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|211061029|gb|FL204116.1|FL204116
EST:     ATTCTATCGATCGGCGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|6342692|gb|AW165516.1|AW165516
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAG-CATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29167933|gb|CB411193.1|CB411193
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|15499585|gb|BI596098.1|BI596098
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAA                         GATCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|19058714|gb|BM737381.1|BM737381
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GNTCTCTTCTCAGACATCAATGCTTATGAGGTGGAGCTTG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAGGTGGAGCTTG
EST: gi|13382241|gb|BG458916.1|BG458916
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29947167|gb|CB816515.1|CB816515
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|211058063|gb|FL204109.1|FL204109
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|32849976|gb|CD989657.1|CD989657
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|13558470|gb|BG549826.1|BG549826
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|6431818|gb|AW172022.1|AW172022
EST:     ATTCTATCGATCGGTGCTGAAGTCAGNGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|13237244|gb|BG355258.1|BG355258
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|29544990|gb|CB605168.1|CB605168
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG
EST: gi|26559456|gb|CA831691.1|CA831691
EST:     ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAG                         GTTCTCTTCTCAGACATCAATGCTTATGAG
genomic: ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaaca ... gcacttgcagGTTCTCTTCTCAGACATCAATGCTTATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTATCGATCGGTGCTGAAGTCAGTGAAGTTGAGGCTGGGAAGAAGgtaaggaacattttatgacttaactcttattgatgcatgctcaaatgctcacttgtgcaaacaagtagcatttttgtgctttgcgtgtgaagtttgttta

- - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - AAGAAG