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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgagtgttcctttttgctgttagggtctttctgtatagtcaatttactgtactacaacttacccttcggaaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGA

Basic information

species Zea mays
transcript GRMZM2G074790_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 5
gtgagtgttgagtgttcctttttgctgttagggtctttctgtatagtcaatttact--gtactaca-acttaccc---------------ttcggaaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGA
||||||    |||| | |||||   | ||||  || | ||| | | ||| | || |  ||| |||  |||||||                || |||||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||| ||||||||||||||||||||||||||||| ||||||||||
gtgagtaccaagtgctgctttt-attattagcctcatactgcagaatcattctatttggtaatacctacttacctaggctgcaacttattttgggaaattggcagGATGGCAAGACATTAGACAATGAGCTTGAAGCGGTACAGGGAATGAAACTTTCCAGAGGCTACATATCTCCTTACTTTGTGACTGATCAGAAGACTCAGA

upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G20560.2 (Glycine max), 3'ss of exon 4
gtgagtgttgagtgttcctttttgctgttagggtctttctgtatagtcaatttactgtactaca-acttacccttcggaaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGA
        | ||      | |    | ||  |  |||  |  | |   || || | || |   | |  ||   ||   ||| |  |||||||| || || ||||| |||||  | ||||  ||| | ||||||||| |  |||||||||||||||||||||| ||| | |||||||| ||||| | ||
-------gtaagcaaatttgtccatttttgtgaacttattacacaacaaagtttcagtccaggatatctataattttaaaactttcagGATGGGAACACTTTGGATAATGAATTGGAAGTGGTAGAAGGAATGAAGTTAACCAGAGGATACATATCTCCTTATTTTATTACTGATCAGAAGACCCGGA

upper sequence: GRMZM2G074790_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G01190.1 (Glycine max), 3'ss of exon 5
gtgagtgttgagtgttcctttttgctgttagggtctttctgtatagtcaatttactgtacta--caacttacccttcggaaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGA
        | ||      | |    | ||  |  |||  |  | |   || || | || |     | ||      |   ||| |  |||||||| || || ||||| ||| || | ||||  ||| | ||||||||| |  ||||||| |||||||||||||| ||| | |||||||| ||||| ||||
-------gtaagcaaatttgtccatttttgtgaacttattacacaacaaaatttcagtccagggtatctataatcttaaaaactttcagGATGGGAACACTTTGGATAATAAGTTGGAAGTGGTAGAAGGAATGAAGTTAACCAGAGGCTACATATCTCCTTATTTTATTACTGATCAGAAGACCCAGA

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|18450792|gb|BM429070.1|BM429070
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGGT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|149014572|gb|EE044215.2|EE044215
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|71438972|gb|DR820022.1|DR820022
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|18649393|gb|BM498212.1|BM498212
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|148966460|gb|EE017469.2|EE017469
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGGATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|78118616|gb|DV537000.1|DV537000
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|18649617|gb|BM498436.1|BM498436
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATNGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|148937683|gb|EC881881.2|EC881881
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|31351656|gb|CD436013.1|CD436013
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGCACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|31350305|gb|CD434662.1|CD434662
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|6021191|gb|AW066119.1|AW066119
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|18450399|gb|BM428677.1|BM428677
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|87153562|gb|DY398351.1|DY398351
EST:     TATCAAAAGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|18648744|gb|BM497563.1|BM497563
EST:     TATCAAANGCTATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|67015320|gb|CO444069.1|CO444069
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|74242338|gb|DT650252.1|DT650252
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|149010196|gb|EE042014.2|EE042014
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
EST: gi|31664231|gb|CD572956.1|CD572956
EST:     TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTT                         GATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG
genomic: TATCAAAAGCCATGGAAAAAGTTGGAAAGGATGGAGTCATTACTATTGTTgtgagtgttg ... aaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctttctgtatagtcaatttactgtactacaacttacccttcggaaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGA
                               aacttac  putative branch site (score: 2)
              tcaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttgagtgttcctttttgctgttagggtctttctgtatagtcaatttactgtactacaacttacccttcggaaattggcagGATGGCAAAACATTGGACAATGAGCTTGAAGCAGTACAGGGAATGAAGCTGTCCAGAGGATACATATCTCCTTACTTTGTGACTGATCAAAAGACTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT