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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcacacggcacatcttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgttgtcaaatggcatatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC

Basic information

species Zea mays
transcript GRMZM2G046743_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
gtacgcacacggcacatcttcgcgcgcgttacggttacggcgaccacaaacaaa--atgaacttttttttgttgtcaaatggcatatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
||  |  |      | |||||     | |       | |   || || ||| ||  | ||| ||  | |   ||     | | || | |||||||| ||||||||||| |||||| |  |||| ||| | |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||
gtcagtcctactatcttcttcatcttcatctgaacgaagaacac-acgaacgaaccaagaaattaatctaactgaattcttgaatttttgcagGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC

upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
-gtacgcacacggcacatcttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgt-tgtcaa-------atggcatatat-gcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
   |   |     |   | ||  | |   |||   ||   |   |     | || |  || || | || || ||| ||       ||  | | | |  |||||| |||||  | |   | || ||| |||| ||| | ||||| || ||||| |||||||| |||||||||||||| |||||| | || || ||  |||| 
aacaactaattttcttcttttttc-caaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT

upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
----gtacgcacacggcacatc---ttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgttgtcaaat---ggcatatatgc-agGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
     |||  |    |    |    |||   |    ||   ||||          |  |   | |  ||  |  | ||   || |   |  |||||||  ||||| || ||||| || || ||| |  | || ||| | || || || |||||| | ||||| |||||||||||||| |||||||| |||||||| || || 
ttgaatacatatgtagttttttaatttcttactacataaatttacttttgatttgattag--taatattcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT

upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S5_176V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacgcacacggcacatcttcgcg----cgcgttacggttacggcg------accacaaacaaaatgaacttttttttgttgtcaaatggca---tatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
||  |  | |  ||| | ||  |     ||  | |  || ||   |          ||         |          ||     ||||||     | ||||||||| || ||  | |  |||||||||||||||||| ||||||||||||||||||| |||||||||||||| ||||||||||||||    || ||||| |||
gtgagggctcctcacgttttgtctaatccgtctcagagtcacacagtttcatgttgcagtttgcggcagtgggcacaagtaacggaatggctattcacatgcagGGGACCGGGAGTGGTGGTGCTGGTGGTGTCGTGGATGATCACGCTGTACACGCTCTGGCAGATGGTGGAAATGCACGAGATGGTCGAGGGGAAGCGTTTC

upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 2
gtacgcacacggcacatcttcgcgcgcgttacggtt--acggcgaccacaaacaaaatg--aacttttttttgttg-tcaaatggcatatatg------cagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
  || |     |    ||  |        | | | |  | |      |||||     |   |||||||    |    |  || |   | | |       |||||| || ||  ||   || || ||  |||||||||||||||| || |||||||||||||| |||||||| |||||||| ||||| || || ||| | || 
--accctagtcgtgtgtcgcccgcaatcctccagctccatgttcttgacaaatggttttccaacttttccaagcaactttaaagatttttttttcgttccagGGGACCGGGGGTCCTTGTTCTTGTACTGTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT

upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25874 (Selaginella moellendorffii), 3'ss of exon 2
gtacgcacacggcacatcttcgcgcgcgtt-acggtt--acggcgaccacaaacaaaatg--aacttttttttgttg-tcaaatggcatatatg------cagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
    |    | ||| ||| ||  |  | || || |    | |      |||||     |   |||||||    |    |  || |   | | |       |||||| || ||  ||   || || ||  | |||||||||||||| || |||||||||||||| |||||||| |||||||| ||||| || || ||| | || 
--gtgtcacccgca-atcctcaagaactttcacagccccatgttcttgacaaatcgttttccaacttttccaagcaactttaaagatttgtttttcgttccagGGGACCAGGGGTCCTGGTTCTTGTACTCTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT

upper sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
gtacgcacacggcacatcttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgttgtcaaatggcatatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
                                 || |||          | ||  |  || |||||| |   ||      | | | | |||||| ||||| |||  ||||||  |  | || |||    ||||||| |||||||| ||||| ||||||||||||||||||||||||   || ||||| |||
---------------------------------gtaacgttcgaatgttataacgtctacattttttagggttctt----cgtttttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTC

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|149000253|gb|EE037406.2|EE037406
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|71428207|gb|DR809257.1|DR809257
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|50336114|gb|CO531240.1|CO531240
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|74244994|gb|DT652908.1|DT652908
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|94478524|gb|EB707482.1|EB707482
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|88757930|gb|DY542071.1|DY542071
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|74235966|gb|DT643880.1|DT643880
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|76285930|gb|DV025498.1|DV025498
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|94473958|gb|EB702916.1|EB702916
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|18963368|gb|BM660397.1|BM660397
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|149078147|gb|EE166895.2|EE166895
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|18963366|gb|BM660396.1|BM660396
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
EST: gi|78092655|gb|DV521029.1|DV521029
EST:     GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTG                         GGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC
genomic: GTCGGCGCCGGCGTGCTCAGCCTTCCCTACGCCTTGTCCGAGCTCGGCTGgtacgcacac ... atatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggcgaccacaaacaaaatgaacttttttttgttgtcaaatggcatatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
           aaacaaaatgaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcacacggcacatcttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgttgtcaaatggcatatatgcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG