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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactagttctctgctctgtgagagacagtacgttgtttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 5
-------gtatactagttctctg-ctctgtgagagacagtacgttgtttaatagtttt--tcctgg--tatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
        | || ||  | | |  |||||| |    ||     |    ||  | | ||  || ||   | ||     ||||   ||  ||||   || |||| ||||||||||||||||| ||||| || |||||||||||||| || ||||| |||||||||||||||||
gtacagtctctattatatatataactctgttaagtccaactattcaaatacaaatcttgttcatgtcctgttctgatatttaaatggatgtataatcatgta-cagACCATCAAGACAAACGTTATCGGAACCCTGAACATGCTTGGACTTGCCAAGAGAGTTGGAGCTAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 5
----gtatactagttctctgctctgtgagagacagtacgtt--gtttaatagtttttcctggtatttcatgattttggtgtttgtaatttc-ctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
      || ||| |||| |  | ||| |  |   | | |||  ||||   || |  |||| |     | |   |    |||| | ||  |   | | |||||| || ||||||||||| ||||| || ||||||||||| || ||||||||  ||||||| || ||
atattaattctacttctgtcatgtgttattgcttgaaagttctgtttttcagctgatccttgagacac-tatctaatatgttaggaaaataatttttacagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAACGAGTTGGGGCAAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 6
-gtatactagttctc-tgc-tctgtgagagacagtacgtt--gtttaatagtttttcctgg--tatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
 || |||    | || ||| ||  |||  || ||| |  |  | |||   ||  ||    |  ||| |    | ||||   |     | || || || ||||| || ||||||||||| ||||| || ||||||||||| || ||||||||| |||| ||||| ||
tgtctacctcctgtcatgcatcattgatcgaaagttctctctgcttatctgtccttgaaagactatatatctaatttgtaatggagtaattacttta-cagACAATAAAGACAAATGTGATTGGCACACTGAACATGCTTGGGCTTGCAAAGCGAGTAGGAGCAAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 5
-----gtatactagttctctgctctgtgagagacagtacgtt--gtttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
      ||| ||| |||| |  | ||| | |    | | |||  ||||   || || |||| |     | |   |    |||| | || |   | | |||||| || ||||||||||| |||||||| ||||||||||| || ||||| ||| ||||||| || ||
tatatttattctacttctgtcatgtgtcatatcttgaaagttctgtttttcagcttatccttgagacac-tatctaatatgttgggaaataatttttacagACAATAAAGACAAATGTGATTGGTACACTGAACATGCTTGGGCTTGCCAAGCGAGTTGGGGCAAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 5
gtatactagttctctgctctgtgagagacagtacgttgtttaat-agtttttcctggtatttcatgattttggtgtttgtaatttcc------tgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
 | | ||| ||   |  |  || |   |   || ||| ||   | ||| |    |||   || |||||  |  |  |||||| |           |||||||| || ||||||||||| ||||| ||| |||||||| |||| ||||| |||||||||||||| ||
-tcttctaatttcttaatgagtaatcaattatatgtttttccctgagtatgctttggacattaatgatggttttccttgtaaatcatgcaatacttaacagACAATAAAGACAAATGTGATTGGCACCTTGAACATGTTGGGGCTTGCCAAGAGAGTTGGAGCCAG

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
-------gtatactagttctctgctctgtgagagacagtacgttgtttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
        ||||  | | ||      | ||           | | | |     |   |    |  |    |||  || | ||||| || ||| | |  |||||||||||||||||||| |||||||| || |||||||| || || || ||  ||||||| || ||
tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagattggtttgaaatttg-gtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAG

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|6637013|gb|AW261285.1|AW261285
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|149097834|gb|EE183762.2|EE183762
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|32909997|gb|CF014809.1|CF014809
EST:     ATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|6020952|gb|AW065880.1|AW065880
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|32850126|gb|CD989807.1|CD989807
EST:     TGCTTGTCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: TGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|40334152|gb|CK368222.1|CK368222
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTGCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGG
EST: gi|22473192|gb|BU037672.1|BU037672
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|213173372|gb|FM186537.1|FM186537
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|26558105|gb|CA830340.1|CA830340
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|21987903|gb|BQ779431.1|BQ779431
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGACTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG                         ACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG
genomic: ACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAGgtatactagt ... cctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG
 gtttaat  putative branch site (score: 4)
                                          tttcctgt  putative PPT
                 tatttcatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactagttctctgctctgtgagagacagtacgttgtttaatagtttttcctggtatttcatgattttggtgtttgtaatttcctgtaacagACCATCAAGACAAATGTTATTGGTACCCTGAACATGCTGGGCCTTGCAAAGAGAGTTGGAGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT