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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattttctcagctctggcattattcttttgaatgtttgtggtgttgcagtgattgtgaaacattgaactcttttgctcacctttgattgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG

Basic information

species Zea mays
transcript GRMZM2G391936_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 10
tcattttctcagctctggcattattcttttgaatgtttgtggtgttgcagtgattgtgaaacattgaactcttttgctcacctttga-ttgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG
| ||  |   ||  ||  |||   |        |  || |        |   | ||  ||   |      |||||| |||  ||||| || |  ||||||||| || || ||||| || || |||||| | ||||||||||| ||||||||||||||| |||| ||||||||| |||| |||||||||
tgatggtgatagtacta-cataggtacgaaattttctttttaaaacagatcaaatgaaaactctctgtaacttttgatcatttttgaattcacttatgcagCCACCGAGATTCAGCTTTTATGATGCTAATAAACCAATGTACACATCACGGAGAAACTTACCGCCATCTATGATCAATAATAGTAAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 10
tcattttctcagctctggcattattcttttgaatgtttgtgg--tgttgcagtgattgtgaaacattgaactcttttgctcacctttgattgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG
|| |||  |    | |   |  | |  |||   ||||    |  ||    ||  | | | |    |  ||       ||| || | ||  | |  | | ||||| || ||||| || || || ||||| | |||||||||||||||||||||||||||| |||||||||| | | |  ||||||| |||
tcttttcatttagtttcaaagaactactttccttgttcaatgattgagagagaaaatcttatttttctaaagaaaaagctgacttctg--taattttttcagCCACCCAGGTTTAGCTTTTATGATGCAGCCAAACCAATGTATACATCACGGAGAAACTTACCACCATCAAAGATTGACAATAGCAAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 10
--------------------------------------------------------------------tcattttctcagctctggca-ttattcttttgaatgtttgtggtgttgcag-----tgattgtgaaacattgaactct-tttgctca--------cctttgattgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG
                                                                    | | ||  | || ||    | ||| ||   |  | |  |||    || ||      | ||| | | |  |  |    | ||| | ||           ||  || |  | | ||||| |||||||| || || |||||||| |  |||||||||||||||||| |||||||| |||||||||| | | |  ||||||| |||
gtgagtgtcaaatcacctcattagtaattagtagaaggtcgtgctagaggtaaacataagaaatgaatttaattattaagttcaaaaacttagtcaactataagcatgtatcatttcatctttttcattttaagatctaaagtcttattttcccagaaaagcttacttctttaattttttcagCCACCAAGGTTTAGCTTTTACGATGCAGCAAAACCAATGTATACATCAAGGAGAAACTTACCACCATCAAAGATTGACAATAGCAAG

upper sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 10
------tcattttctcagctctggcattattcttttgaatgtttgtggtgttgcagtgattgtgaaacattgaactcttttgctcacctttgattgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG
       ||  |  ||  | | | ||   |||||||  | | |  || |    || | ||    |    ||  | |   |   | || |  |  |  ||  |  |||||      || ||||||||||| || |  |||||||| ||||||||| |||||||||| |||||||| |   |  ||||   ||||
gtaaagacaaatattct-cccagacaactttcttttccaagatattgtt--cacaatcatatatagttgttatattaaata--taacttacgtctacaccttttagCCTGGGGCATTTAGTTTCTACGACGCGGCAAAACCAATATATACATCAAGGAGAAACCTGCCACCATCAAAAATAGACAACTCTAAG

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|32934983|gb|CF039795.1|CF039795
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|13126505|gb|BG317075.1|BG317075
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTA
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTA
EST: gi|211232745|gb|FL322840.1|FL322840
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|110195335|gb|EC877232.1|EC877232
EST:     TTGGAACTATTAAGTCTTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|32934981|gb|CF039793.1|CF039793
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|71429962|gb|DR811012.1|DR811012
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|71323466|gb|DR798382.1|DR798382
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|50335821|gb|CO530947.1|CO530947
EST:     CTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: CTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|31362917|gb|CD447274.1|CD447274
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
EST: gi|78103575|gb|DV522003.1|DV522003
EST:     TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG                         CCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG
genomic: TTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAGgtacgtgttt ... aactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagtgattgtgaaacattgaactcttttgctcacctttgattgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG
             aaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattttctcagctctggcattattcttttgaatgtttgtggtgttgcagtgattgtgaaacattgaactcttttgctcacctttgattgaactatgcagCCTCCAAGGTTCAGTTTCTACGATGCTGACAAACCAATGTATACATCACGGAGAAACCTACCACCATCTATGGTCAACAATAGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA