RetrogeneDB ID: retro_ogar_1984

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873579.1:2410536..2412870(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000029793
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFKM
• Ensembl ID: ENSOGAG00000005501
• Aliases: None
• Description: phosphofructokinase, muscle [Source:HGNC Symbol;Acc:8877]

Sequence

>retro_ogar_1984
ATGACCCATGAAGAGCACCATGCAGCCAAAACTCTGGGGATCTGCAAAGCCATTGCTGTGTTAACCTCTGGTGGAGATGC
CCAAGGAATGAATGCTGCTGTCAGGGCTGTGGTTCGAGTTGGTATCTTTACTGGTGCCCATGTCTTCTTTGTCCATGAGG
GTTATCAAGGCCTGGTGGATGGGGAAGATCACATCAGGGAAGCCACCTGGGAGAGCGTTTCCATGATGCTTCAGCTGGGA
GGCACGGTGATTGGAAGTGCCCAGTGCAAGGACTTTCGGGAACGAGAAGGACGACTCCGAGCTGCATATAACCTGGTGAA
GCGTGGGATCACCAATCTGTGTGTCATCGGGGGGTGATGGCAGCCTCACCGGGGCTGACACCTTCCGTTCAGAGTGGAGT
GACTTGTTGAGTGACCTCCAGAAAGCAGGTAAGATCACAGATGAGGAGGCTAAGAAATCCAGCTACCTGAACATCGTGGG
CTTGGTTGGCTCAATTGACAATGACTTCTGCGGCACTGATATGACCATTGGTACTGATTCTGCTCTGCACCGGATCATAG
AAATTGTAGATGCCATCACCACCACTGCCCAGAGCCACCAGAGGACATTTGTGTTAGAAGTGATGGGCCACCACTGTGGA
TACCTAGCCCCTGTTACCTCTCTCTCCTGTGGGGCCAACTGGGTTTTTATTCCTGAATGTCCACCAGATGATGACTGGGA
GGAACACCTTTGTCACCGACTCAGTGAGACAAGGACCCGAGGTTCTCGTCTGAACATCATCATTGTGGCTGAGGGTGCAA
TTGACAAGAATGGCAAGCCAATCACCTCAGAAGACATCAAAAATCTGGTGGTAAAGCGTCTGGGATATGACACCTGGGTC
ACCGTCTTGGGGCATGTACAGTGGGGAGGGACACCATCAGCCTTTGACTGAATCCTGGGCAGCAGGATGGGCGTGGAAGC
AGTGATGGCACTTTTGGAGGGGACCCCAGATACTCCAGCCTGTGTAGTGAGCCTGTCTGGTAACCAAGCCGTGCACCTGC
CCCTCATGGAGTGTGTCCAGGTGACCAAAGACGTGACCAAGGCCATGGAGGACAAGAAATTTGATGAAGCCATGAAGCTG
AGAGGCCGGAGCTTCATGAACAACTGGGAGGTGTATAAGTTCTAGCCCATGTCAGACCCCCAGTATCTAAGAGCGCTTTG
CACACAGTGGCCGTGATGAATGTGGGGGCCCCAGCTGCAGGCATGAATGCTGCTGTTCGCTCCACTGTGAGGATCGGCCT
CGTCCAGGGCAACCAAGTGCTGGTTGTACATGATGGCTTCGAGGGCCTGGCCAAGGGTCAGATTGAGGAAGCTGGCTGGA
GCTATGTTGGGGGCTGGACTGGTCAAGGAGGTTCTAAACTTGGGACTAAAAGAACTCTACCCAAGAAGCACTTGGAACAG
ATCAGTGCCAACATAACGAAGTTTAACATCCAGGGCCTTGTCATCATTGGGGGCTTTGAAGCTTACACGGGGGGCCTGGA
GCTGATGGAGGGCAGGAAGCAGTTTGATGAGCTCTGCATCCCATTTGTGGTCATTCCTGCTACTGTCTCCAACAACGTCC
CTGGCTCAGACTTCAGCATTGGGGCCGACACAGCACTCAATACCATCTGCACGACCTGTGACCGCATCAAGCAGTCAGCA
GCAGGCACCAAGCATCGGGTGTTTATCATTGAGACTATGGGTGGCTACTGTGGCTACCTGGCCACCGTGGCAGGACTGGC
AGCTGGGGCTGATGCCGCCTACATTTTTGAGGAGCCCTTCACCATTCGAGACCTGCAGGCAAATGTTGAACATCTGGTGC
AAAAGATGAAAACAACTGTGAAAAGGGACTTGGTGTTAAGGAATGAAAAGTGCAATGAGAACTACACCACTGACTTCATC
TTCAACCTGTACTCGGAGGAAGGGAAGGGCATCTTCGACAGCAGGAAGAATGTGCTCAGTCACATGCAGCAGGGTGGGAG
TCCAACTCCATTTGACAGGAATTTTGCCACTAAGATGGGTGCCAAAGCTATGAACTGGATGTCTGGGAAAATCAAAGAGA
GTTACCGCAATGGGCGGATCTTCGCCAATACTCCAGACTCAGGCTGTGTTCTGGGGAAGCGTAAGAGGACCCTGCTCTTC
CAACCAGTGACTGAGCTGAAGGACCAGACTGATTTTGAGCATCGAATCCCCAAGGAACAATGGTGGCTGAAGCTGAGGCC
CATCCTTAAAATCCTGGCCAAGTACGAGATTGACTTGGATACCTCCGACCATGCCCACCTGGAGCACATCACTCGGAAGC
GGTCTGAGGAAGCT

Alignment

ORF - retro_ogar_1984 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.51 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTHEEHHAAKTLGIGKAIAVLTSGGDAQGMNAAVRAVVRVGIFTGARVFFVHEGYQGLVDGEDHIREATW
          MTHEEHHAAKTLGI.KAIAVLTSGGDAQGMNAAVRAVVRVGIFTGA.VFFVHEGYQGLVDGEDHIREATW
Retrocopy MTHEEHHAAKTLGICKAIAVLTSGGDAQGMNAAVRAVVRVGIFTGAHVFFVHEGYQGLVDGEDHIREATW

Parental  ESVSMMLQLGGTVIGSARCKDFREREGRLRAAYNLVKRGITNLCVIGG-DGSLTGADTFRSEWSDLLSDL
          ESVSMMLQLGGTVIGSA.CKDFREREGRLRAAYNLVKRGITNLCVIGG.DGSLTGADTFRSEWSDLLSDL
Retrocopy ESVSMMLQLGGTVIGSAQCKDFREREGRLRAAYNLVKRGITNLCVIGG>DGSLTGADTFRSEWSDLLSDL

Parental  QKAGKITDEEAKKSSYLNIVGLVGSIDNDFCGTDMTIGTDSALHRIIEIVDAITTTAQSHQRTFVLEVMG
          QKAGKITDEEAKKSSYLNIVGLVGSIDNDFCGTDMTIGTDSALHRIIEIVDAITTTAQSHQRTFVLEVMG
Retrocopy QKAGKITDEEAKKSSYLNIVGLVGSIDNDFCGTDMTIGTDSALHRIIEIVDAITTTAQSHQRTFVLEVMG

Parental  RHCGYLALVTSLSCGADWVFIPECPPDDDWEEHLCRRLSETRTRGSRLNIIIVAEGAIDKNGKPITSEDI
          .HCGYLA.VTSLSCGA.WVFIPECPPDDDWEEHLC.RLSETRTRGSRLNIIIVAEGAIDKNGKPITSEDI
Retrocopy HHCGYLAPVTSLSCGANWVFIPECPPDDDWEEHLCHRLSETRTRGSRLNIIIVAEGAIDKNGKPITSEDI

Parental  KNLVVKRLGYDTRVTVLGHVQRGGTPSAFDRILGSRMGVEAVMALLEGTPDTPACVVSLSGNQAVRLPLM
          KNLVVKRLGYDT.VTVLGHVQ.GGTPSAFD.ILGSRMGVEAVMALLEGTPDTPACVVSLSGNQAV.LPLM
Retrocopy KNLVVKRLGYDTWVTVLGHVQWGGTPSAFD*ILGSRMGVEAVMALLEGTPDTPACVVSLSGNQAVHLPLM

Parental  ECVQVTKDVTKAMEDKKFDEAMKLRGRSFMNNWEVYK-LLAHVRPPVSKSALHTVAVMNVGAPAAGMNAA
          ECVQVTKDVTKAMEDKKFDEAMKLRGRSFMNNWEVYK..LAHVRPPVSKSALHTVAVMNVGAPAAGMNAA
Retrocopy ECVQVTKDVTKAMEDKKFDEAMKLRGRSFMNNWEVYK<VLAHVRPPVSKSALHTVAVMNVGAPAAGMNAA

Parental  VRSTVRIGLIQGNRVLVVHDGFEGLAKGQIEEAGWSYVGGWTGQGGSKLGTKRTLPKKNLEQISANITKF
          VRSTVRIGL.QGN.VLVVHDGFEGLAKGQIEEAGWSYVGGWTGQGGSKLGTKRTLPKK.LEQISANITKF
Retrocopy VRSTVRIGLVQGNQVLVVHDGFEGLAKGQIEEAGWSYVGGWTGQGGSKLGTKRTLPKKHLEQISANITKF

Parental  NIQGLVIIGGFEAYTGGLELMEGRKQFDELCIPFVVIPATVSNNVPGSDFSIGADTALNTICTTCDRIKQ
          NIQGLVIIGGFEAYTGGLELMEGRKQFDELCIPFVVIPATVSNNVPGSDFSIGADTALNTICTTCDRIKQ
Retrocopy NIQGLVIIGGFEAYTGGLELMEGRKQFDELCIPFVVIPATVSNNVPGSDFSIGADTALNTICTTCDRIKQ

Parental  SAAGTKRRVFIIETMGGYCGYLATMAGLAAGADAAYIFEEPFTIRDLQANVEHLVQKMKTTVKRGLVLRN
          SAAGTK.RVFIIETM...........GLAAGADAAYIFEEPFTIRDLQANVEHLVQKMKTTVKR.LVLRN
Retrocopy SAAGTKHRVFIIETMXXXXXXXXXXXGLAAGADAAYIFEEPFTIRDLQANVEHLVQKMKTTVKRDLVLRN

Parental  EKCNENYTTDFIFNLYSEEGKGIFDSRKNVLGHMQQGGSPTPFDRNFATKMGAKAMNWMSGKIKESYRNG
          EKCNENYTTDFIFNLYSEEGKGIFDSRKNVL.HMQQGGSPTPFDRNFATKMGAKAMNWMSGKIKESYRNG
Retrocopy EKCNENYTTDFIFNLYSEEGKGIFDSRKNVLSHMQQGGSPTPFDRNFATKMGAKAMNWMSGKIKESYRNG

Parental  RIFANTPDSGCVLGMRKRTLLFQPVTELKDQTDFEHRIPKEQWWLKLRPILKILAKYEIDLDTSDHAHLE
          RIFANTPDSGCVLG.RKRTLLFQPVTELKDQTDFEHRIPKEQWWLKLRPILKILAKYEIDLDTSDHAHLE
Retrocopy RIFANTPDSGCVLGKRKRTLLFQPVTELKDQTDFEHRIPKEQWWLKLRPILKILAKYEIDLDTSDHAHLE

Parental  HITRKRSSRS
          HITRKRS...
Retrocopy HITRKRSEEA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1984 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009035	1 retrocopy	retro_cfam_1463,
Microcebus murinus	ENSMICG00000009077	1 retrocopy	retro_mmur_970,
Otolemur garnettii	ENSOGAG00000005501	1 retrocopy	retro_ogar_1984 ,