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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagatttgaatcatcatcaaatagtgtattgctagaaagtcatgagaacaaattttatttgacaatacttccaaattgagggtgttctgcatgga...

Basic information

species Zea mays
transcript GRMZM2G174644_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 5'ss of exon 2
GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagatttgaatcatcatcaaa-tagtg----tattgctagaaagtcatgagaacaaattttatttgacaatacttccaaattgagggtgttctgcatgga
| || | || |||||||| ||||||||||||||||| |||||||||||||| ||||| ||||  || |||||||  ||| ||||||| || ||||| || |    ||||   ||| |||| ||||     |||| || ||||   |  || |     ||    |||| ||  | | |  ||  | || |      |   
GTTGGTCGGCTATGAAGGACTTGAAGTTATTAACCCAGATGGAGGCACAGAAGATGCGGAAGCTGAGGCTTTGAGAGGGCGATGGAAACAAGAGgtgagaatcactgaaatgtcaacaaaatagtaattttatttcttgaaa--tacaagcatgttattagactgaccattgtactagtttatgtgtatgtcaatt---

upper sequence: GRMZM2G174644_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 5'ss of exon 2
GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagatttgaatcatcatcaaatagtgtat-tgctagaaagtcatgagaacaaat--tttatttgacaatacttccaaattgagggt-gttctgcatgga
| ||||||||||||||||  | |||||||| ||||| || ||||||| ||| ||||| ||||||||||||   |  || ||||||||| |||||| | |  | ||||   |||  |  |||    | | |  ||||   | ||       |||  || | || | | |  ||  |  ||||   |   |  || |   
GTTGCTTGGTTATGAAGGTGTGGAAGTTATAAACCCAGAGGGAGGCAAAGAAGATGCGGAAGAAGAAGCTCAAAGAGGAAGATGGAAGGAGGAGgcatgttgctttg--ccattctttaatcccttttgtattagatttttattttttttaatggttgaattcatacttatttta--ttgacacttagtgggcctatg
















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|22491096|gb|BU051019.1|BU051019
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|19351392|gb|BM895924.1|BM895924
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|13150716|gb|BG321038.1|BG321038
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211272002|gb|FK970185.1|FK970185
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAAT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAAT
EST: gi|74244334|gb|DT652248.1|DT652248
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211271996|gb|FK970179.1|FK970179
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GAC-GTGATAGCTACTGGAAGATGATGCACAAATACATAG
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAG
EST: gi|211271998|gb|FK970181.1|FK970181
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|148954837|gb|EC900310.2|EC900310
EST:     GCGCAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|149078287|gb|EE167049.2|EE167049
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|71326510|gb|DR799932.1|DR799932
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|94475418|gb|EB704376.1|EB704376
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|148995971|gb|EE035219.2|EE035219
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|28909493|gb|CB331845.1|CB331845
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|76011657|gb|DT938827.1|DT938827
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211271999|gb|FK970182.1|FK970182
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|148940242|gb|EC885014.2|EC885014
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|78116426|gb|DV534813.1|DV534813
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|71326507|gb|DR799931.1|DR799931
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|149084040|gb|EE173435.2|EE173435
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211272003|gb|FK970186.1|FK970186
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATTGCACAAATACATAGGATCAGATGT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGAT-GCACAAATACATAGGATCAGATGT
EST: gi|18659308|gb|BM500269.1|BM500269
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAACTACTGGAAGATGATGCACAAATACATANGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagatttgaatcatcatcaaatagtgtattgctagaaagtcatgagaacaaattttatttgacaatacttccaaattgagggtgttctgcatgga

- - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG