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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtactctatttctgtgctcgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC

Basic information

species Zea mays
transcript GRMZM2G114172_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 5
gttagtactctatttctgtgctcgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC---
                   | | ||| |  |    || |||| |  ||||   | |  ||||  ||||  ||||   ||||| |||| |  | ||||||||||||   || ||||  ||||| || ||||||||||| || |||||||| || ||||||||||||||||| ||||| |||||||| |||| || ||   | |   
-------------------gttagtagtggcgtggtactgtgaatttgtgactgattctcattgaattatttgctcattgcttctgtttctttcatatgcagTAC---AATGAAACAAACACAATCATGTTTGATGACCTCAGAAGGAACTTTGTCATGAATCCACAGAATGGTCTTGTGATCAAACCATACAAGAGGACCCATT

upper sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 4
lower sequence: AT4G06599.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagtactctatttctgtgct-cgtattaccaattta-atgtggacctgtgt-taggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC
          ||||| | |     | ||   || || | |  || | ||   | |   | || || |||||  |||  | |   ||||| |||       |||||| ||| |||      ||||| |||||||||||||| ||||| ||||||||||| |||||||| || ||||||||    |||||||| || |||||||| |
---------gtatttatatatcatgcatcctcatttgacacatgaatcttgatctttttttttatgtaattgattggtgttg--tcctgactt------gtgcagTTCTATAACCCTGGTAACACGATAATGTTTGATGACCTAAGGAGGAATTTCGTAATGAATCCTCAAAACGGTCTAACAATCAAGCCGTTTAGGAAAGCTC

upper sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv12s0035g00640.t01 (Vitis vinifera), 3'ss of exon 5
gttagtactctatttctgtgctcgtattaccaa---tttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctc-catatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC
 ||   |  |||| |      | | ||||       |||  ||||| ||       | |||||  ||| ||       |  || |  | |||| |    | |||||| |||||    ||| |||||||| ||||||||||| ||  |||| ||||| || ||||| |||||||||||| |    ||||||||||||||||| || |
-ttcaaatgctatatagaaaattgaattattgcatttttcttgtgggcccaat---gatcttc--ctacttgacaatagactggtggtatcttgttatttttgcagTTCTACAGTTCAAAAAACACCATCATGTTTGATGACCTTCGAAGAAATTTTGTGATGAACCCACAGAACGGTTTGACAATCAAGCCATTCAGGAAGGCTC

upper sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ35150 (Selaginella moellendorffii), 3'ss of exon 5
gttagtactctatttctgtgctcgtattaccaatttaatgtggacctgtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC
                               ||     |  |  |||   |||| ||| | | | |||  ||     ||| |    ||||       | ||||  ||      ||| ||||| || ||||| |||||||| |  ||||| ||||| ||||||||||| || ||||||||||||  ||| || |  ||||| |
-----------------------------gtaaagcgtttagatccttctttagatct-cttatcattttttaaattttggtttcttctttctttgctacagTTTTATGGACCAAACAACACGATCATGTTGGATGATCTCAAGAGGAACTTCGTGATGAATCCACAAAATGGTCTCGTGATCCGGCCTTTTAAAAAAGCTC

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|211170844|gb|FL475252.1|FL475252
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|20337038|gb|BQ172668.1|BQ172668
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGACCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|37383817|gb|CF628944.1|CF628944
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|86470825|gb|DY237195.1|DY237195
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|37377229|gb|CF625199.1|CF625199
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC
EST: gi|5791422|gb|AI978214.1|AI978214
EST:     AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAG                         TACTACAACGAAAAGAACACCATAATGTTTGATGACCTAAGAAGGAATTTC
genomic: AGACTTTTGACTGCAAGCCTCTTGGTGTCATTTGGGCTCAGTTCCCTGAGgttagtactc ... ccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttaggtcttcatctaattccttgccgcttgctcctgtcttctccatatgcagTACTACAACGAAAAGAACACCATAATGTTTGATGATCTAAGAAGGAATTTCGTCATGAATCCACAGAACGGTCTCGTGATCAAGCCATTCAGGAAAGCGC
             atctaat  putative branch site (score: 3)
                   ttccttgccgcttgct  CT-rich tract
             atctaatt  TA-rich tract