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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgccttgacaatattatggagcaagatgttagttgcgactgagtcaagatgtgatcttgttcattcatacttctcactctgaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT

Basic information

species Zea mays
transcript GRMZM2G095348_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
gtgcgccttgacaatat--tatggagcaagatgttagttgcgac---tgagtcaagatgtgat--cttgttcattcatacttctcactctgaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
||  |  |  ||||| |  |||| ||   ||||||| |  | |    ||  |    ||| | |   |||| || | ||  |||| |  ||||||    ||||||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||
gtctgtttc-acaatctcttatgcagtg-gatgttattcacaatatatggctttttatgaggtgatttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT

upper sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------------------gtgcgccttgacaatattatggagcaagatgttag--ttgcgactgagtcaagatgtgatcttgttcattcatacttctca-ctctgaaattgta--gATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
                                                                                    |  || |||  | || ||||      | ||||  | | |    |  |   || |   | | || | |    |   | | |||||   |||||  ||||||||  || ||||| ||||| || ||||| || || || |  ||||| ||||||||||| || || || |||||||||||||||||| | ||  |||
gtgagatattatgtgcttcgatgttcttctattggcattatgtacgtaaagaaattctatgaaaaaaaaaggaagagttttaatccactcgact-tgttgtggaatgcttttttagggtagtgttctaaacgt-atatcgccatattgagttgatcagatgagctctgtctttgtatagATATGGAACTTGGGTTCACCAGAGCCCAACTTTACCCTCGAGGCTCATCAGAAGGGTGTCAACTGCGTGGAATACTTCACTGGTGGTGACCGACCACATT
















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|18655044|gb|BM499849.1|BM499849
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18654986|gb|BM499791.1|BM499791
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCA
EST: gi|32930849|gb|CF035661.1|CF035661
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|22489991|gb|BU049914.1|BU049914
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAA-CTTCAC-CTTGA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGA
EST: gi|18655016|gb|BM499821.1|BM499821
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAG
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAG
EST: gi|18649626|gb|BM498445.1|BM498445
EST:     CAAAGGATATTAACACTTTAGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCT
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCT
EST: gi|32933566|gb|CF038378.1|CF038378
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|22489999|gb|BU049922.1|BU049922
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCAC-CTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|89106409|gb|DY576626.1|DY576626
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18661996|gb|BM501688.1|BM501688
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGACCGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTGGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
EST: gi|18450688|gb|BM428966.1|BM428966
EST:     CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGC-CGCACTACAAAG                         ATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA
genomic: CAAAGGATATTAACACTTTTGCAAGTGCATCTCTTGATCGCACTACAAAGgtgcgccttg ... gaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgactgagtcaagatgtgatcttgttcattcatacttctcactctgaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
                                   ttctcac  putative branch site (score: 2)
                                              aaattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgccttgacaatattatggagcaagatgttagttgcgactgagtcaagatgtgatcttgttcattcatacttctcactctgaaattgtagATATGGAGTTTAGGTTCTCCAGATCCAAACTTCACACTTGATGGACATCAAAAGGGTGTCAATTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG