RetrogeneDB ID: retro_pabe_321

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:174749299..174751331(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: WDR48
• Ensembl ID: ENSPPYG00000014001
• Aliases: None
• Description: WD repeat-containing protein 48 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAW8]

Sequence

>retro_pabe_321
ATGGCGGCCCATCACCGGCAGAAGACAGCAGGGCGGAGGAAAGTGCAGGTTTCCTATGTTATTCAAGATGAAGTGGAGAA
GTACAACCGAAATGGAGTCAATGCTCTGCAGCTGGATCCAGCACTAAATAGACTTTTCACAGCCAGTCGAGACTCTATCA
TAAGAATATGGAGTGTCAATCAGCACAAGCAAGATCCGTATATAGCATCTATGGAACACCATACTGATTGGGTAAATGAC
ATTGTACTCTGTTGTAATGGGAAAACATTAATATCTGCTTCTTCTGACACAACAGTAAAAGTATGGAATGCACACAAGGG
ATTTTGCATGTCAACATTAAGGACACATAAGGATTACGTAAAGGCCTTAGCATATGCCAAGGATAAAGAACTAGTAGCAT
CAGCTGGGTTGGACAGATAAATATTCCTTTTGGATGTGAATACTCTAACAGCATTGACTGCCTCAAATAACACTGTCACA
ACTTCTTCTTTAAGTGGAAACAAAGATTCCATTTATAGCCTGGCCATGAATCAACTGGGAACAATCATTGTATCAGGGTC
CACTGAAAAGGTGTTAAGGGTATGGGATCCAAGAACATGTGCAAAACTAATGAAGCTTAAAGGGCACATGGATAATGTGA
AGGCATTGCTATTAAACAGAGATGGCACGCAATGCCTTTCAGGCAGTTCTGATGGGACAATTCGCCTTTGGTCCCTTGGC
CAGCAGAGATATATAGCAACATACCGAGTCCATGATGAAGGTGTTTGGGCGCTGCAAGTCAATGATGCCTTCACATATGT
GTATTCTGGTGGAAGGGACAGGAAGATTTATTGTACAGACCTAAGAAACCCTGACATTCGGGTGCTAATTTGTGAAGAAA
AAGCACCAGTTCTCAAGATGGAGCTTGATAGATCAGCTGATCCTCCTCCTGCAATTTGGGTTGCAACAACTAAGTCTACA
GTAAATAAATGGACTTTGAAAGGAATTCATAATTTTAGAGCCTCTGGAGATTATGACAATGACTGTACAAATCCTATAAC
ACCTCTTTGTACACAACCTGACCAGGTTATTAAGGGGGGGTGCTAGTATTATTTAGTGCCACATTCTTAATGATAAGAGA
CATATATTAACCAAAGATACCAATAATAATGTGGCATATTGGGATGTATTGAAGGCATGTAAAGTTGAAGATCTGGGCAA
AGTGGATTTTGAAGATGAAATTAAGAAAAGATTTAAAATGGTGTATGTGCCAAATTGGTTCTCAGTAGACTTAAAAACAG
GGATGTTAACTATTACTTTGGATGAAAGTGATTGTTTTGCTGCCTGGATTTCTGCAAAAGATGCGGGTTTCAGCAGCCCT
GATGGGTCAGATCCAAAATTGAATTTAGGAGGACTTTTACTCCAAGCACTCCTGGAATATTGGCCTAGAACACCTATGAA
TCCAATGGATGAAGAGGAAAATGAAGTAAACCATGTAAATGGGGAGCAGGAGAACCGAGTGCAGAAGGGAAATGGATATT
TTCAAGTGCCCCCACACACACCCGTGATCTTTGGTGAAGCTGGAGGTCGCACACTGTTCGGGCTGCTCTGCCGAGATTCT
GGGGGTGAGACTGAGTCTATGCTTCTTAATGAAACAATGCCACAATGGGTAATTGACATCACTGTGGATAAAAATATGCC
CAAATTCAACAAAATTCCTTTCTACCTCCAACCTCATGCATCTTCAGGAGCAAAAACCTTAAAAAAAGATAGACTCTCTG
CTAGTGACATGCTCCAAGTCCAAAAAGTTATGGAACATGTTTATGAAAAAATTATCAACTTGGATAATGAGTCTCAAACT
ACTGGCTCTTCTAATAATGAAAAACCAGGAGAATAGGAAAAAGAAGAAGATATTGCTGTGTTGGCAGAGGAGAAAATTGA
ACTTTTGTGCCAGGACCAGGTTTTGGATCCAAATATGGACCTTCGAACAGTGAAACACTTCATATGGAAGAGCGGTGGAG
ACCTCACCCTCCATTACCGTCAGAAGTCCACG

Alignment

ORF - retro_pabe_321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAHHRQNTAGRRKVQVSYVIRDEVEKYNRNGVNALQLDPALNRLFTAGRDSIIRIWSVNQHKQDPYIAS
          MAAHHRQ.TAGRRKVQVSYVI.DEVEKYNRNGVNALQLDPALNRLFTA.RDSIIRIWSVNQHKQDPYIAS
Retrocopy MAAHHRQKTAGRRKVQVSYVIQDEVEKYNRNGVNALQLDPALNRLFTASRDSIIRIWSVNQHKQDPYIAS

Parental  MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDRQ
          MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDR.
Retrocopy MEHHTDWVNDIVLCCNGKTLISASSDTTVKVWNAHKGFCMSTLRTHKDYVKALAYAKDKELVASAGLDR*

Parental  IFLWDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHT
          IFL.DVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGH.
Retrocopy IFLLDVNTLTALTASNNTVTTSSLSGNKDSIYSLAMNQLGTIIVSGSTEKVLRVWDPRTCAKLMKLKGHM

Parental  DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRCIATYRVHDEGVWALQVNDAFTHVYSGGRDRKIYCTD
          DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQR.IATYRVHDEGVWALQVNDAFT.VYSGGRDRKIYCTD
Retrocopy DNVKALLLNRDGTQCLSGSSDGTIRLWSLGQQRYIATYRVHDEGVWALQVNDAFTYVYSGGRDRKIYCTD

Parental  LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWILKGIHNFRASGDYDNDCTNPITPLC
          LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKW.LKGIHNFRASGDYDNDCTNPITPLC
Retrocopy LRNPDIRVLICEEKAPVLKMELDRSADPPPAIWVATTKSTVNKWTLKGIHNFRASGDYDNDCTNPITPLC

Parental  TQPDQVIK-GGASIIQCHILNDKRHILTKDTNNNVAYWDVLKACKVEDLGKVDFEDEIKKRFKMVYVPNW
          TQPDQVIK.GGASII.CHILNDKRHILTKDTNNNVAYWDVLKACKVEDLGKVDFEDEIKKRFKMVYVPNW
Retrocopy TQPDQVIK>GGASII*CHILNDKRHILTKDTNNNVAYWDVLKACKVEDLGKVDFEDEIKKRFKMVYVPNW

Parental  FSVDLKTGMLTITLDESDCFAAWVSAKDAGFSSPDGSDPKLNLGGLLLQALLEYWPRTHVNPMDEEENEV
          FSVDLKTGMLTITLDESDCFAAW.SAKDAGFSSPDGSDPKLNLGGLLLQALLEYWPRT..NPMDEEENEV
Retrocopy FSVDLKTGMLTITLDESDCFAAWISAKDAGFSSPDGSDPKLNLGGLLLQALLEYWPRTPMNPMDEEENEV

Parental  NHVNGEQENRVQKGNGYFQVPPHTPVIFGEAGGRTLFRLLCRDSGGETESMLLNETVPQWVIDITVDKNM
          NHVNGEQENRVQKGNGYFQVPPHTPVIFGEAGGRTLF.LLCRDSGGETESMLLNET.PQWVIDITVDKNM
Retrocopy NHVNGEQENRVQKGNGYFQVPPHTPVIFGEAGGRTLFGLLCRDSGGETESMLLNETMPQWVIDITVDKNM

Parental  PKFNKIPFYLQPHASSGAKTLKKDRLSASDMLQVRKVMEHVYEKIINLDNESQTTSSSNNEKPGEQEKEE
          PKFNKIPFYLQPHASSGAKTLKKDRLSASDMLQV.KVMEHVYEKIINLDNESQTT.SSNNEKPGE.EKEE
Retrocopy PKFNKIPFYLQPHASSGAKTLKKDRLSASDMLQVQKVMEHVYEKIINLDNESQTTGSSNNEKPGE*EKEE

Parental  DIAVLAEEKIELLCQDQVLDPNMDLRTVKHFIWKSGGDLTLHYRQKST
          DIAVLAEEKIELLCQDQVLDPNMDLRTVKHFIWKSGGDLTLHYRQKST
Retrocopy DIAVLAEEKIELLCQDQVLDPNMDLRTVKHFIWKSGGDLTLHYRQKST

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.20 RPM
SRP007412_cerebellum	0.00 RPM	34.17 RPM
SRP007412_heart	0.00 RPM	13.94 RPM
SRP007412_kidney	0.00 RPM	19.56 RPM
SRP007412_liver	0.00 RPM	13.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_321 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_321 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000007796	1 retrocopy	retro_pabe_1932,
Pongo abelii	ENSPPYG00000014001	2 retrocopies	retro_pabe_320, retro_pabe_321 ,
Pongo abelii	ENSPPYG00000019140	1 retrocopy	retro_pabe_274,