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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatggaattcaattctaaggatccaaacggggactaagaggaaataattttctgaagcttcaaagttttgtaattatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG

Basic information

species Zea mays
transcript GRMZM2G147884_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 8
gaatggaattcaattctaaggatccaaacggggactaagaggaaataattttctgaagcttcaaagttttgtaat------tatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
       ||   | | || |   |  || |     |  || |   ||||||||||   |  || | ||||| |||      |||||||| || || |||| |  ||||||| || ||||| ||||||||||| |||||||||||||| ||||| || ||  |||||||||||||||| || |||||||| ||||| ||||| ||||
-----atatctgaattta-gttccttaatgaattttttgatgctttaattttctgctaccacatatttttgcaatataatttatttgttcattctgttggatatagGATGGCAAGATAGAAGCAGAAGTAAAACTTACTGGAATTCTTAGTTTGGGAGCTCTGATGCCTGGGGAATCAAGAAAATATGGTACAACCATTGCTCCTG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA01G03200.1 (Glycine max), 3'ss of exon 1
gaatggaattcaattctaaggatccaaacggggactaagaggaaataattttctgaagcttcaaagttttgtaattatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
                      | |||||     |        | |||||   | || |   ||       | | |||||| |  | ||| |  || |||||||| |||||||| || || || ||||| || ||||||||||||||||| || |||   || || |||    | ||||||||||| |||||||| ||||
---------------------gttcaaacataagc------atattaattggttaaatcactaat------tgagtatttgct--ttctcattctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 7
---gaatggaattcaattctaagg---atccaaacggg-gactaagaggaaataattttctgaagcttcaaagttttgtaattatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
   | ||  |  |  | | |  ||   ||   || |    |  |  || | || | ||  | ||    | ||   ||||   |||||| |    ||| |  || |||||||| |||||||| || || || ||||| || ||||||||||||||||| || |||   || || |||    | ||||||||||| |||||||| ||||
caggcattcatattgactttgtggtgaatttcaatgttcaaacataagcatattaattggttaaatcactaa---ttgtg--tatttgct--ctctccttctttcagGATGGAAAAATAGAAGCTGAGGTCAAGCTCACGGGAATTCTCAGTTTAGGAGCATTGCAACCAGGTGAAAGTCGAAAATATGGCACGACTATTGCACCTG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G38990.1 (Glycine max), 3'ss of exon 7
gaatggaattcaattctaaggatccaaacggggactaagaggaaataattttctga----agcttcaaagttttgtaattatttgttg--atcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
      | | |   | || || |     | |    |||  |   | |  |     |    || ||      | | ||||| ||||||   ||  || |  ||||||||||| |||||||| ||||| || ||||| || ||||||||||| ||||| || |||   || || ||| |  | |||||||||||||| ||||| ||||
------attccttatttatggctttctgctgtatttaaatgtttaaacctcaaacatattagtttgttgtctctataattctttgtttgtattttccttcttgcagGATGGAAAAATAGAAGCAGAGGTCAAGCTCACAGGAATTCTCAGCTTAGGAGCATTGCAACCAGGTGAAACTCGAAAATATGGCACAACCATTGCACCTG

upper sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT2G42490.1 (Arabidopsis thaliana), 3'ss of exon 7
-gaatggaattcaattctaaggatccaaacggggactaagaggaaataattttctgaagcttcaaagttttgtaa----ttatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
 |    |||| | | | |    ||         || |   ||     |  |||||  |  ||  |||     ||     |||| | ||||   ||||   || ||||||||||||| || || |||||||| |||||||| || ||||||||||| ||  ||  ||| || ||| |  | || || || || |||||||| ||||
agtgctgaatccgagtttc---atttgttttctgatttgtagttt-catctttctagatatttgaagaccaatatcattttatgtcttgaatgtctta-ctgtagGATGGGAAAATCGAAGCTGAAGTAAAACTTACTGGTATCCTCAGTTTAGGAGCTCTGCAGCCAGGTGAAACTCGAAAGTACGGTACTACTATTGCTCCTG

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|91873704|gb|EB403661.1|EB403661
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGGAATTCTCAGTTTAGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGG-AATTCTCAGTTTAGG
EST: gi|32919574|gb|CF024386.1|CF024386
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|60342955|gb|DN209928.1|DN209928
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|211285882|gb|FL038895.1|FL038895
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAKATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGCTTAGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAA-ATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGG
EST: gi|67028492|gb|CO457241.1|CO457241
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|67010284|gb|CO439033.1|CO439033
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGCTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|31348944|gb|CD433301.1|CD433301
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|47961763|gb|CN844472.1|CN844472
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|211285883|gb|FL038896.1|FL038896
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGCTTAGGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
EST: gi|211285880|gb|FL038893.1|FL038893
EST:     TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTTCTCAGCTTAGG
genomic: TCTGTACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATT-CTCAGTTTAGG
EST: gi|32831046|gb|CD970724.1|CD970724
EST:     ACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAG                         GATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG
genomic: ACAGTTGCAAACTATGAGTATGGTTTTTACTGGCACTTCTATCAGgtaatatttc ... ttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttctgaagcttcaaagttttgtaattatttgttgatcctcttggttgcagGATGGGAAAATAGAGGCAGAAGTAAAGCTTACTGGAATTCTCAGTTTAGGGGCCTTGATGCCTGGGGAATCGAGGAAATATGGCACAACTATTGCCCCTG
                                  tgttgat  putative branch site (score: 4)
                                        tcctctt  CT-rich tract
              ttcaaagttttgtaat  TA-rich tract