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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagtgctccaaacatggatagtgtgtgactagtgtattaaaattcccggcatctggaattctgattgaactattggcgctgacttatttttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG

Basic information

species Zea mays
transcript GRMZM2G004459_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 3'ss of exon 3
tgtagtgctccaaacatggatagtgtgtgac-tagtgtattaaaattcccggcatctgg--aattctgattgaactattggcgctgacttattt-ttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG
     ||| |   | |    || |  ||| | || |    || |||||| |  ||   |  |  | ||  | |||||  |    | | ||||   |  |  ||||| || ||||||||||| |||||||||||||| || ||||||||||| || || || || |||||||||   ||| |||| ||||| || |||||||| |
--ctatgcacttgataatcttaattggtgccctactaagatagaattccagatattgtgctaggtttgggttaacta--gaatataatttatgaatgctttcagGTTCCCGAGGTCTTCTACTATGCCCAGAAGGCGGTGCTTCACCCAACAGCACCTCTATTTGATCAAGAGGCGCAATCTCTAAAGCCACGGTGTGTGAGGG

upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 3'ss of exon 3
--tgtagtgctccaaacatggatagtgtg---tgactagtgtattaaaattcccggcatctggaattctgattgaactattggcgctgacttatttttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG
  |    |  |     |||| ||  | ||      |   || ||||||| ||| | |||   |   |    |  | |||       |  | ||| |||   ||||||   |||||||||||||||||| ||||| ||||| ||| ||||||| ||||| || || ||||| |||  |||    || |||   || ||| |||| |
aattagttaattatcgcatgaattatttgaaccatcagatgcattaaaagtccagacatt--gtgctagtctctagctaactataattgcgtatgttt---gcagGTTTATGAGGTCTTCTATTATGCACAGAAAGCAGTGCTTTACCCAACAGCTCCTCTATTTGATCAGGAGGCACAGATGCTAAAGTTACGCTGTATGAGGG

upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G29580.1 (Glycine max), 3'ss of exon 3
--------tgtagtgctccaaacatggatagtgtgtgactag------tgtattaaaattcccggcatctggaattctgatt-------gaactattggcgctgacttatttttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG
        | || |   |    ||   | | |   ||  | |      | | ||||| |||    ||  |  | || | |||         || ||| ||  | |  | || || | | |||| || || || ||||| ||||| |||||||| || ||||| ||||| |||||  | || |||||||||| |||| |||| ||||||||||| ||| |||
gtatcttttatactaaccattgcaatcaaactacttgttttgacatcttattttaaacttctgatcaattatattttttattttgtttcatacaatttgctattatattttcttgttgaagGTCCCCGAAGTTTTCTACTATGCACAGAAGGCCGTGCTTCATCCAACAGCTCCATTATTTGATCAAGAGTCACAAACTCTAAAGCCTCGATGCGTGCGAG

upper sequence: GRMZM2G004459_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G37730.1 (Glycine max), 3'ss of exon 3
---tgtagtgctccaaacatggatagtgtgtgactagt-----------gtattaaaattcccggcatctggaattctgatt-------gaactattggcgctgacttatttttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG
   | |  ||  | || | | | ||       ||| ||            | |||||  | | ||    |   ||| |||||         || ||| ||  | |  | || || | | |||| ||||| || ||||| ||||| || ||||| || ||||| ||||| |||||  | || |||||||||| |||| |||| ||||||||||| ||| |||
gtatcttttgtactaaccgttgctatcaaactacttgttttgacatcttattttaaagcttctggtcaattatattttgattttgttttatacaatttgctattatattttcttgttgaagGTCCCTGAAGTTTTCTACTATGCACAAAAGGCTGTTCTTCATCCAACAGCTCCATTATTTGATCAAGAGTCACAAACTCTAAAGCCTCGATGCGTGCGAG

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|31361614|gb|CD445971.1|CD445971
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|78084949|gb|DV513342.1|DV513342
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211289495|gb|FL459844.1|FL459844
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211153232|gb|FL160597.1|FL160597
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211289494|gb|FL459843.1|FL459843
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|91053299|gb|EB163717.1|EB163717
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|60339673|gb|DN206646.1|DN206646
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211153243|gb|FL160608.1|FL160608
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|60340644|gb|DN207617.1|DN207617
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|60354705|gb|DN221678.1|DN221678
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|31358133|gb|CD442490.1|CD442490
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccggcatctggaattctgattgaactattggcgctgacttatttttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG
                                 cgctgac  putative branch site (score: 3)
                                       cttattttttt  CT-rich tract
                                    tgacttattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagtgctccaaacatggatagtgtgtgactagtgtattaaaattcccggcatctggaattctgattgaactattggcgctgacttatttttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCTCCGCTCTTCGATCAAGAGTTACAAGCTCTGAAGCCTCGATGTGTGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC