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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatagaactcgatgtcattttgtgccacattctgatttatcttatatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT

Basic information

species Zea mays
transcript GRMZM2G120579_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120579_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g14440.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------------------------gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatagaactcgatgtcattttgtgccacat---tctgatttatcttatatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT---
                                                                                           ||      |   |  | | | | |       ||    ||  ||||  ||   | |   |||| |||| ||   |  |   |||||| |||||| | |||||||||||||  ||||||||||||||||||||||||| ||||||| |||||||| | ||| | |||| |||||| ||   || |||||| |||| | |||  ||   
gtaaagcttatcataccgctgtattttcgctgtgctatctaattctcgtgaaaccatgtatattgatggagcatagcctttattcttcccaagaaaaaaaaatctaaatatcgatgaaatttct---tacaaggttagcacttagcagtatgtaatttggtataatttctatctgatatatcttgtttcttcagGTTCTTGCTAATAGCTTGCGCTATTTCTTGAGGAGGCCGACGACAGAGGAGGGCAGTTACTAGGCAGATAAATA--CAGGAAGCCCCCCA-CCTTCAGATACT

upper sequence: GRMZM2G120579_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G02580.1 (Glycine max), 3'ss of exon 9
------------------------------------------------------------------gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatag-aactcgatgtc---attttgtgccacattctgatttat-cttat-atctt-cagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT-
                                                                  || ||  |  |    | | ||  ||||  ||  |||      |  ||| |||   | |  |||       ||||    |  | |  |||| ||  |||| ||||  |||||||||  ||| |||||| | |||||||||||||| |||||||| |||||  | || || |     |  |  | ||    |    | |      |  ||| 
gtaactttaatcttgtaaagaatgataaaaatcaaaatggcatcatacattgaagaggccatgcaagttggt-tctaactactaatgaagtttgatcatctagtggtgtacttcacatgccagcaagattctttagtttttgaactgaattagattcatgtttatcatctggcagGTTCTTGCTAACAGCTTGAGATATTTCTTGAGGCGTCCGACAACTGAGGAATCTAGTTTTTGAGTGG-CACTTCATGGAAAGTAGTGCAGGACATTGTATT

upper sequence: GRMZM2G120579_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G23440.1 (Glycine max), 3'ss of exon 9
-------------------------------------------------------------------gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatag-aactcgatgtc---attttgtgccacattctgatttat-cttat-atctt-cagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT-
                                                                   || ||  |  |    | | ||| ||||  ||  |||         ||| |||   | |  |||       ||||    |  | |  |||| ||  |||| ||||  |||||||||  ||| |||||| | |||||||||||||| |||||||| |||||  | || || |     | ||  |  |    |    | |      |  ||| 
gtaactttaatcttgtaaagaatgataaaaaaccaaaatggcatcatacattgaagaggccatgcaagttggt-tctaacttctaatgtagtttgatcatctagtggtggacttcacatgccagcaagattctttagtttttgaactgaattagattcatgtttatcatctggcagGTTCTTGCTAACAGCTTGAGATATTTCTTGAGGCGTCCGACAACTGAGGAATCTAGTTTTTGAGTGG-TACTTCTTGGAAAGTAGTGCAGGACATTGTATT

upper sequence: GRMZM2G120579_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv09s0018g01780.t01 (Vitis vinifera), 3'ss of exon 9
gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatagaactcgatgtcattttgt-gccacattctgatttatcttatatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT-
  |   | |  | |     |  |      |   ||        | ||    ||| |       ||    ||| ||   ||| | |     |  |  |   ||||||||| ||||||| || || |||||||||||||| ||  |||||||||| || || || |   |   |  | ||  |     ||| | |   |  |||  
--aacagagttgagtttggtagt-cgagctgagctgagggttggttttgtttaggaacattcatctccatgttgcagaattttaacactaccaaacttggcagGTTCTTGGTAATAGTTTACGGTATTTCTTGAGGCGACCATCAACAGAGGAGGCAAGTTTTTGAGCCATTCTA-GACGAAATCACCTTCAAGACTGATTACA

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|32922805|gb|CF027617.1|CF027617
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|32864535|gb|CF004217.1|CF004217
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|32865391|gb|CF005073.1|CF005073
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|211018355|gb|FL222709.1|FL222709
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|211354510|gb|FL449970.1|FL449970
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGGGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|32923305|gb|CF028117.1|CF028117
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|32922818|gb|CF027630.1|CF027630
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|29544320|gb|CB604700.1|CB604700
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|211541735|gb|FL481473.1|FL481473
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
EST: gi|211018356|gb|FL222710.1|FL222710
EST:     AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAG                         GTTCTTTCTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC
genomic: AATTCCATGTCAGCTACAGGGGCAGAACACTGACCGAGGCTTTACAACAGgtaggcgtgc ... atatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatagaactcgatgtcattttgtgccacattctgatttatcttatatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT
                               ttctgat  putative branch site (score: 3)
                                              tatcttc  putative PPT
                                    atttatcttatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcgtgcagtgcccattgttgttttttcccctatacacctggttctcatagaactcgatgtcattttgtgccacattctgatttatcttatatcttcagGTTCTTTGTAATAGCTTGCGCTATTTCTTGAGGCGGCCGACAACAGAGGACGCCAGCTTCTAGCCAGATAGATGATCATGAAGCCTCCCAACTTTCTTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC