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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggccttaatgtgcagcttcagttcgtgtagatttctgtgtgttgcatcacacatttatatttttactgcatgtttatgatagatcaatgagctgtttgtccttaacaaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC

Basic information

species Zea mays
transcript GRMZM2G440916_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G440916_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g51790.1 (Oryza sativa), 3'ss of exon 3
gttggccttaatgtgcagcttcagttcgtgt-agatttctgtgtgttgcatcacacatt---tatatttttac--tgcatgtt----tatgatagatca-atgagctgtttgtccttaacaaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC
            ||||| || |||| | | | |||||    | | || ||| |  ||||   |||  |||| |  ||||||      |||  ||   || | ||||   |             | |     |  |    | | || | ||||| || ||  ||||  || |  ||||  | || |||||||| |||| ||||||||| ||| | |  || || ||| | || ||||||||||||||||||||||| || ||| || ||||||| |
------------gtgcacctccagtccattttagattcagctcttttacatgatccattccttatcattttcctttgcatgccatgatattgtaatccagaggagccactcacttacccttttatcgtgaatctattcctgatttctgttgcttttgtgctcaac-tctgttcagTTTCTTCCTCAAGACCGAGTATGTGAATTTGCGAAGTTGACACCTATCCAATTACTGGAAGAGACTGAAAAGGCTGTTGGAGATCCTAATCTACCTATCC

upper sequence: GRMZM2G440916_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G34020.1 (Glycine max), 3'ss of exon 4
gttggccttaatgtgcagcttcagttcgtgtagatttctgtgtgttgcatcacacatttatatttttactgcatgtttatgatagatcaatgagctgtttgtccttaacaaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC
                                       | || ||  | || ||||||| ||  ||      |||   | |||  |   |   || ||| ||||      |   |||||            ||| || |    | |||      | | | ||||| || || |||||| |||| | ||| ||||||||| ||| |||  |||||||||| |||||||| ||||||||||||||||| ||  |  | ||    |
------------------------------------agggagtattttaacatacatttaaataattt-----tgtccctaatactttgtttttctttttctcct------agctaactga-----------ttgcttggaacctttgt------cttttgtagTTTTTACCGCAAGACAGGGTCTGTGAGTTTGCAAAGTTAACTCCTGTTCAACTTCTGGAAGAGACCGAAAAGGCTGTTGGTGATCCACAGCTTCCAGAGC

upper sequence: GRMZM2G440916_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0064g00180.t01 (Vitis vinifera), 3'ss of exon 4
gttggccttaatgtgcagcttcagttcgtgtagatttctgtgtgttgcatcacacatttatatttttactgcatgtttatgatagatcaatgagctgtttgtccttaacaaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC
                                                         ||||   |||    || |    | ||   |     | ||  ||||| ||           || |     |    ||| |||| |  ||  | |       |   |||||||||||||||||| |||| ||||||||||| ||| ||| |||  | |||||||||||||| || ||||||||||||||||| ||| |  ||||  | |
--------------------------------------------------------cttatgagtttgaatcagggccttcatct-tgggctaccttcttgtctttt-------ttccttttcctttcattcttatttttcgttttggggttggtggtggttagTTCTTGCCACAAGACAGGGTCTCTGAATTTGCTAAGTTAACTCCTGTGCAACTTCTAGAAGAAACAGAAAAGGCTGTTGGTGATCCTCAACTACCAGTCC

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|211293504|gb|FL223351.1|FL223351
EST:     TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAG                         TTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
genomic: TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAGgttggcctta ... acctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
EST: gi|166678800|gb|EG058255.1|EG058255
EST:     TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAG                         TTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
genomic: TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAGgttggcctta ... acctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
EST: gi|211293505|gb|FL223352.1|FL223352
EST:     TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAG                         TTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
genomic: TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAGgttggcctta ... acctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
EST: gi|211276647|gb|FL478165.1|FL478165
EST:     TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAG                         TTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
genomic: TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAGgttggcctta ... acctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
EST: gi|211445136|gb|FL478285.1|FL478285
EST:     TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAG                         TTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA
genomic: TTATTGACGTGATTAAGAAATTCAATATTCAAGTTAACAACTTAACTCAGgttggcctta ... acctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC
                ctttaac  putative branch site (score: 3)
                                            cacctctct  putative PPT
                 tttaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggccttaatgtgcagcttcagttcgtgtagatttctgtgtgttgcatcacacatttatatttttactgcatgtttatgatagatcaatgagctgtttgtccttaacaaaagcaactgtggagctttaacttgttttgctgttctgtgcaacacctctctagTTCTTGCCACAAGACCGGGTATCTGAATTTGCAAAGCTAAGTCCCATTCAACTTCTAGAAGAGACTGAAAAGGCTGTTGGTGACCCTGATTTACCTATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT