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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagattctagtgcactacctcatattctccaattgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG

Basic information

species Zea mays
transcript GRMZM2G107089_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 3'ss of exon 3
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagattctagtgcactacctcatattctccaattgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
                  ||    |||  |  |   |   ||  || || |     ||||||  ||||    ||             |||  ||| |||| ||||||||| || | ||  |||| | ||||| || |     |||| ||||| ||||| ||||||||||||||||| |||||||| |  ||||| |||||||| || |||||||| ||| ||||||||||||| ||||| ||||| ||||
----------------gtttgttgaatgctaatcatt---gcacaagttcct---tcatgcacttgataacacaaa-----------ttgg-aaagaatggaagattctaatgtaata--tcatctgctccattttt-----ctcttcagGCAATGCAAATGATTGATGTATATACAAAATTTGCATACGAGCAAGCTGCAATCCCTGTTATTCCGGGTCGAAAATCAAGAGTGGAAACGTTTGCTGGTG

upper sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G29890.1 (Glycine max), 3'ss of exon 5
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagattctagtgcactacctcatattctccaattgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
                                                 || |   | |   ||| | | ||     || || |||  |  || | | || |  ||  |||||    ||  |||  | | |||           |||||||| || |||||||||||  | ||||||| |||||| | |||||| |||||||||||||||||| ||||| ||||||| | ||| ||||||||||| ||||
------------------------------------------------gtccacttcttttctgtcaagatg---ataaatc-tttactagtata-attgcataatcttagtg----acgacattctgttcaa-----------ctgcagGCTATACAGATGATTGACATCTATACCAGATTTGCGTATGAGCAAGCTGCAATACCAGTTATTACAGGTCGAAAATCTAAAGTGGAAACATTTGCCGGTG

upper sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G24670.1 (Glycine max), 3'ss of exon 5
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagatt--ctagtgca-ctacctcatattctc--caat-tgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
                                                                           | |  || |||||    | |  |  |||  ||  |||||| |  | | | || ||     |||| |  | ||   |||||||| || |||||||||||  | ||||||| |||||| | |||||| ||||||||||| ||| || ||||| ||||||| | ||| ||||||||||| ||||
-------------------------------------------------------------------------gtgcacatcttttctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcagGCTATACAGATGATTGACATCTATACCAGATTTGCTTATGAGCAAGCTGCAATACCTGTTGTTACAGGTCGAAAATCTAAAGTGGAAACATTTGCTGGTG

upper sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G52520.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagattctagtgcactacctcatattctccaattgtta---ttgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
                                                                 | | || |   | ||  |  | | |  ||    || |   || |  ||   |||       |  | |||  |||   |||   |||||||||  |||||||| ||  | || |||| |||||| ||||||||  ||||||| || |||||||||||| |||||||||   |||| || ||||| ||||
-----------------------------------------------------------------gtttgttctctatag--agctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCAATTCCTGTTATTCCAGGTCGAAAATCAAAGTTAGAGACTTTTGCTGGTG

upper sequence: GRMZM2G107089_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 3'ss of exon 5
gttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttct-tgataaacaatgaaagattctagtgcactacctcatattc-tccaattgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
                                                                       | |   | |  || | | ||| || || |   |   | |  |    |  ||  | ||| |  ||  | |  |   ||||||||  | |||||||||||||| ||||| |||||||| | |||||| ||||||||||| |||||| ||||| ||||||||| ||| || |||||||| ||||
-----------------------------------------------------------------------gtattcatgatatctatctgaaaaccactcctaatctttcttatgttttcttgtcttcatttaacagattgtaaactgcagGCATTACAGATGATTGATGTCTATACAAAATTTGCTTATGAGCAAGCTGCAATACCTGTTATTACAGGTCGAAAATCAAAAGTGGAGACATTTGCTGGTG

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|149110507|gb|EE294163.2|EE294163
EST:     GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAG                         GCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
genomic: GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAGgttagttttc ... tgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
EST: gi|76018748|gb|DT945918.1|DT945918
EST:     GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAG                         GCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
genomic: GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAGgttagttttc ... tgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
EST: gi|148950310|gb|EC895869.2|EC895869
EST:     GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAG                         GCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
genomic: GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAGgttagttttc ... tgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
EST: gi|71760344|gb|DR958281.1|DR958281
EST:     GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAG                         GCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCCTGC
genomic: GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAGgttagttttc ... tgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGC-TGC
EST: gi|6194519|gb|AW146623.1|AW146623
EST:     GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAG                         GCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA
genomic: GGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAGgttagttttc ... tgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgaaagattctagtgcactacctcatattctccaattgttattgctctgcagGCGATGCAGATGATTGATGTATATACCAAATTTGCCTTTGAGCATGCTGCAATACCAGTTATTCCAGGTAGAAAATCAAGAGTAGAAACATTTGCGGGTG
                                            ttgctct  CT-rich tract
                                    aattgttatt  TA-rich tract