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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctacttcttttattgcaattgaaatatgttaatagatctggttagtctatgactctatgtccttatttttctgcatggctaatgtattttctgtgattgattaataattgtcgaactaatgttattagaaagagttatggatcgtgaagttattctaagtacattcatctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG

Basic information

species Zea mays
transcript GRMZM2G142640_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 2
gtaagtttctacttcttttattgcaattgaaatatgttaatagatctggttagtctatgactctatgtccttatttttctgcatggctaatgtattttctgtgattgattaataattgtcga-actaatg--ttattagaaagagttat---ggatcgtgaagttattctaag---tacattcatctc---cttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG
||||||| ||   | | || |||   ||  |||||| |  |||||    |||||    | |  | | ||||     | ||  | |     |   ||||  || | || |    ||  ||  | |  ||||  |||  |   ||   |||     ||   |||| ||||  ||    ||| || || |    | | |||||| || |||||||| || || ||||||||||| ||||| ||||| |||||| | ||||| ||||||||||| |||
gtaagttcctgtgtatatt-ttgttgtttcaatatgattgtagattgttttagt----gcccttttatcctgtgcatgctctaggctatgtagttttttggttaatggtagtaaaaggttaatagcaatgatttaccaatgagtactatttcatatttggaaggtatttcaactattacttttatttttatcctacaggacagAGCTTTGCCGTTTTAGTGGCCAGAAGATATATCCAGGGAAGGGCATTCGCTTTATTCGTGCTGATTCACAG

upper sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagtttctacttcttttattgcaattgaaatatgttaatagatctggttagtctatgactctatgtccttatttttctgcatggctaatgtattttctgtgattgattaataattgtcgaactaatgttattagaaagagttatggatcgtgaagttattctaagtacattcatctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG
                                                                   || ||  | |  || | | || |  | ||||| |||     | ||  ||  |     |   || |||   |   |  |||  || |    ||||| |   |  | |          ||||||||| ||||| || ||||| || ||||||||||| || || | ||| ||||| ||||||||  |||||||||||
-------------------------------------------------------------------tcatttctatcatgta-gactgagat-ttttcagtg-----tcaaagatcatttggtt---gtcatttctagttgcaatgtctcatttgtttattatctatgaaat---------acagGACGGAGCTTTGTCGTTTCAGTGGACAGAAGATTTACCCAGGAAGAGGAATTAGGTTTATCCGATCTGATTCTCAG

upper sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT2G36620.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagtttctacttcttttattgcaattgaaatatgttaatagatctggttagtctatgactctatgtccttatttttctgcatggct---aatgtattttctgtgattgattaataattgtcgaactaatgttattagaaagagttatggatcgtgaagttattctaagtacattcatctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG
                                                                                  ||||||   ||||| | | |||||| || ||  | |||||   || |  |||          ||| |||||  | |   ||  | |   |   || |    ||| ||||| || |||||||| ||||| |||||||| ||||| ||||| | ||| || |||||||||||  | || ||||||
---------------------------------------------------------------------------aaatgagatggctttgaatgtgtgtcctgtgactgtttg-tgattgt--gaccagggttg---------gttttggattatca--ctaaaccattgattatctttgtattgtagGACTGAGCTTTGCCGATTCAGTGGCCAGAAAATTTACCCTGGTAGAGGGATCAGATTTATCCGATCGGACTCTCAG

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|9952995|gb|BE639578.1|BE639578
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|67024843|gb|CO453592.1|CO453592
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAC                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|24767969|gb|CA403102.1|CA403102
EST:     GTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: GTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|60339160|gb|DN206133.1|DN206133
EST:     GGCTGAGAACATGGTGCTGAA                         GACGGAATTTTGCCGCTTCAGCGGCCAGAAGATTTTTCCTGGGAAAGGCAT
genomic: GGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|78025581|gb|DV493968.1|DV493968
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|86470272|gb|DY236642.1|DY236642
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|211180303|gb|FL410015.1|FL410015
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGC-GSCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|78027478|gb|DV495865.1|DV495865
EST:     AGTTGGTGAAGG-TTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|32858460|gb|CD998141.1|CD998141
EST:     TTGAGGCTGAGAACATGGGGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: TTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|32865027|gb|CF004709.1|CF004709
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|211133239|gb|FL429638.1|FL429638
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCTGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|16137348|gb|BI894213.1|BI894213
EST:     AGTTGG-GAAGGTTTCTTGAGGCTGAGAACATGG-GCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|22819537|gb|BU499627.1|BU499627
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGG-CAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|31360690|gb|CD445047.1|CD445047
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|21760033|gb|BQ635574.1|BQ635574
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|22715310|gb|BU197696.1|BU197696
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|211530300|gb|FL400695.1|FL400695
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGC--SCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|31353813|gb|CD438170.1|CD438170
EST:     AAAATATGTAGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AAAATATGTAGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|15188208|gb|BI417185.1|BI417185
EST:     AGTTGGTGAAGGTTTC-TGAGGCTGAGAACATGGGGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|60393960|gb|DN226830.1|DN226830
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|60342152|gb|DN209125.1|DN209125
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|32858470|gb|CD998151.1|CD998151
EST:     TTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTCGGGAAAGGCA
genomic: TTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCT-GGGAAAGGCA
EST: gi|31354798|gb|CD439155.1|CD439155
EST:     AAAATATGTAGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AAAATATGTAGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|60345067|gb|DN212040.1|DN212040
EST:     GTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: GTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|15177592|gb|BI398531.1|BI398531
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGA-TTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
EST: gi|60343076|gb|DN210049.1|DN210049
EST:     AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAA                         GACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT
genomic: AGTTGGTGAAGGTTTCTTGAGGCTGAGAACATGGTGCTGAAgtaagtttct ... ctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagaaagagttatggatcgtgaagttattctaagtacattcatctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG
                                        ttcatctcctt  CT-rich tract
                          ttattctaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctacttcttttattgcaattgaaatatgttaatagatctggttagtctatgactctatgtccttatttttctgcatggctaatgtattttctgtgattgattaataattgtcgaactaatgttattagaaagagttatggatcgtgaagttattctaagtacattcatctccttgcagGACGGAACTTTGCCGCTTCAGCGGCCAGAAGATTTATCCTGGGAAAGGCATTAGATTTATCCGTGCTGATTCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT