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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

Basic information

species Zea mays
transcript GRMZM2G143356_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcct--caaatggtgacttactg----aactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
|||||| | ||| | | ||||  | |||  | | |  |||   ||  |  || ||    |  || |   |  |||         | ||||||||| || ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || ||| |
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
|||| |||||||   |       |  |  | |       ||     | | |       | |   || ||  ||      |||||||||| || || || ||||| || ||||| ||||||||||||||||| ||  |||| ||||| |||||||     |||||  | || || ||||| || ||
gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaa----ctcactcgtgttgcttt------ctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S245_10V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------gtatgcctctttctctg-----tatggctaatagtcaacttgaaataagactataagagagtcctc-----aaatggtgacttactgaac-----tgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                                                | || |||     ||||      ||   |    |  |||   | ||    ||     ||    |||     |||  || || |     ||     ||||||||| || || |||||||| || ||||||||||||||||||||||| |||   ||    ||  ||   ||    ||||| ||||| || |||   |||||
gtatttgctgacgctaaaccctcgcagcattgtgaagcatgttcgatcgaataccttgcaatctgagcttcattcttgtaggaaaacaaaacattttgctgatctagttctctcttgctaaaaagtaacctttgtgacctttgtgcagTTGGAGGTCTCCTGAATGCAACTTTTGGAAATGCAACTGAAATGATTATTTGTATCATGGCCCTGCGGAAGAATATGATACGAGTTGTACAGTTATCACT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S79_95V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------gtatgcctctttctctgtatg-gctaatagtcaacttgaaataagacta--taagagagtcctcaaatggtga-------cttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                                            || ||| | | |  |  | || |||       |     || |  |  |   | |   | | |||  | |  ||       |||    |  ||||||||| || || |||||||| || |||||||||||||||||| |||| |||    |    ||| |    ||    ||||| ||||| || ||    |||||
gtgattgccgaagttcgaatgttgctgccttatgaagcatattggtttgcatttcttgcaatctgtgctgcagaataggggcaagtgtgtttggctgattcaattctctgacgaagaaactgatctttgctatttgcagTTGGAGGTCTCCTGAATGCGACCTTTGGAAATGCAACTGAAGTGATTATTTGTGTCATGGCTCTCCGGAAGAACATGATACGAGTTGTACAATTATCACT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
----gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctc----------aaatggtgacttactgaact-gcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCAT-TGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
     || |    |  |     ||||      |     ||||  |||  ||   |       |||          |||   ||  ||  |  ||| |||||||| || ||||||||||| || ||||| |||||||| |||||||| || ||||  || ||||||    ||   |||||| ||||| || |||   |||||
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCAT-TGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ12361 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcctctttctctgta-tggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                ||| |   | |||  |   |    || | |     || || |  ||   |  ||  |  ||    |||||| ||||||||||||||||| || ||||||||||| || || ||||| ||  | || |  ||| ||   ||||| |||||||| || || |||| ||| ||
----------------gtaataaattatacccttttctcgatcacaaagagagtgaatggtcctttt-tgtttctct----tgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT

upper sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ33760 (Selaginella moellendorffii), 3'ss of exon 1
gtatgcctctttctctgta-tggctaatagtcaacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                ||| |   | |||  |   |    || | |     || || |  ||   |  ||  |  ||    |||||| ||||||||||||||||| || ||||||||||| || || ||||| ||  | || |  ||| ||   ||||| |||||||| || || |||| ||| ||
----------------gtaataaattatacccttttctcgatcacaaagagagtgaatggtcttttt-tgtttctct----tgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT

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|148951918|gb|EC897694.2|EC897694
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
EST: gi|211103676|gb|FL335622.1|FL335622
EST:     GCAGCTTGCAGTATACACTGGTCCCACAG                         G
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcag-
EST: gi|211103676|gb|FL335622.1|FL335622
EST:     GCAGCTTGCAGTATACACTGGTCCCACAG                         G
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcag-
EST: gi|211203502|gb|FL354146.1|FL354146
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTAACATT-GGAAAATGCA-CTGGAATGATCAT
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTA-CATTTGGAAA-TGCAACTGAAATGATCAT
EST: gi|148952030|gb|EC897816.2|EC897816
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
EST: gi|149080754|gb|EE169818.2|EE169818
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
EST: gi|211019237|gb|FL365611.1|FL365611
EST:     GCAGCTTGCAGTATACACTGGTCCCACAG                         TTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATT
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTT-GGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATT
EST: gi|149075868|gb|EE164419.2|EE164419
EST:     GCAGCTTGCAGTATACACTGGTCCAACAG                         TTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG
genomic: GCAGCTTGCAGTATACACTGGTCCAACAGgtatgcctct ... tgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacttgaaataagactataagagagtcctcaaatggtgacttactgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT
                                      gacttac  putative branch site (score: 2)
       aaataagactataa  TA-rich tract