RetrogeneDB ID: retro_ogar_516

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873522.1:26907441..26909086(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTNNA1
• Ensembl ID: ENSOGAG00000011865
• Aliases: None
• Description: catenin (cadherin-associated protein), alpha 1, 102kDa [Source:HGNC Symbol;Acc:2509]

Sequence

>retro_ogar_516
CACCACAGAAACATAAACTTCACATGGAACCCCAAAAGTCTAGAGATCAGGACTCTGCCAGTTGAAAGACTGCTGGAGTC
TCTTATTACACAGGTTACCAATAGTAAGGGGCCTTCTAATAAGAAGAGAGATTGTTCTAAGAAGACCCATGTTTTGGCTG
CATCTGTTGAACAAACAACTGAAAATTTTTTTAAGGGGCATAAAATTGCAAAGGAGAGTCAATTTCTGAACGAGGAGCTT
GTAGCTGCCAAAGAAGACGTTCCCAAACAAGGTGATCTGATGAAGACTGTTGACGGAGAGTTCACAGATGATCCCTGCTC
TTCTGTGAACGAGGCAACAAGGTTCAGGCAGCTGGAGCTTTACTCTCTGCTATTACTCGACTGCTGATTTGGGCTGACAG
GGCAGATGTCTACAAATTACTTATTCAGCTGAAAGTTGTGGAAGATGGGATCTTGAAACTGAGGAATGCTGGCAATGAAC
AAGATTTAGGAATACAGAATAAAGCCCTGAAACCTGAAGTGAATAAACTGAACATTATGGCAGCCAAAAGACAACAGGAA
CTGAAAGATGTTGGCCATCGTGATCAGATGGCTGCAGCTAGAGGAATCCTGTAGAAAATGTTCCGATCCTCTATACTGCA
TCCCAGGCATGCCTACAGCACCATGATGTTGCAGCCTATAAGGCTAACAGAGACCTGATATATAAGCAGCTGCAGCAGGC
AGTCACAGGCATTTCCAACGCAGCCCAGCCACTGCCTCCGGCAATGCCTCCCAACACCAGGGAGGAGGTGGAGGAAAACT
GGCGTATGTGCTCAATAACTTTGATAAACAAATCATACGGAGCTTCAGTGAGAAGCACTTTAGGTCTTCCCTGGAGGCAT
GCCTGGAAAGCATCATTAGTGGGGCTGCCCTAATGGTGGAATCATCCTGTACACGTGATGACCAGAGTGGGCCAATGGTG
GCAGAGTGCAATGCTATCCGCCAGGCCCTGCAGGACCTGCTTTCAGAGTACACGGGCAATGCCGGACCAAAAGAAATAAG
TGATGAGCTCAATTCTGCTATAGATAAATGACCAAGAAGACCAGGGACTTGCGTAGGCTGCTCCACAAAGCTGTCACTGA
CCACATTTCAGATTCTTCCCTGGAAACCAATGTTCCCCTTTTAGTATTAACTGGAGCTGCAAAGAATGGAAATGAGAAAG
AAGTTAAGGAATATGCCCAAGTTTTCCATGAACAGGCCAACAAATTGATTGAGGTGCCAACTTGGCCCGTTCCATCTCAA
ATAATGAAGAAGGCATCAAACTTGTTCATATGTCTGCAAGCCAGTCAGAAGCCGTCTGTCCTCAGGTTATCAATGCTGCA
TTGGCTTTAGCAGCAAAACCAGAGTAAACTGGCCCAAGGAGAATATGGATCTTTTAAAAGAACAGTGGGAAAAATAAGTC
CATGTTCTCACAGATGCCATTGATGACATTACTTCCATTAATGACTTCTAGTTGTCTCAGAGAATCATGGCTTGGAAGAT
GTGAACAAATGTGCATTTGCTCTCTAAGAGAAAGATGTGGATGGCCGGACCACACAGCTGGTGCAATTTGAGGCTGGGCA
GCCCGGGTCATTCACGTAGTCACCTCAGAGATAGACAACTATGAA

Alignment

ORF - retro_ogar_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.63 %
• Parental protein coverage: 61.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  HTGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLD
          H..NINF.W.PKSLEIRTL.V....E.L.....T.V.TNSKGPSNKKR..SKK.HVLAASVEQ.TENF..
Retrocopy HHRNINFTWNPKSLEIRTLPV----ERLLESLITQV-TNSKGPSNKKRDCSKKTHVLAASVEQTTENFF-

Parental  KGDKIAKESQFLKEELVAAVEDVRKQGDLMKTAAGEFADDPCSSV-KRGNMVRAARALLSAVTRLLILAD
          KG.KIAKESQFL.EELVAA.EDV.KQGDLMKT..GEF.DDPCSSV..RGN.V.AA.ALLSA.TRLLI.AD
Retrocopy KGHKIAKESQFLNEELVAAKEDVPKQGDLMKTVDGEFTDDPCSSV<ERGNKVQAAGALLSAITRLLIWAD

Parental  MADVYKLLVQLKVVEDGILKLRNAGNEQDLGIQYKALKPEVDKLNIMAAKRQQELKDVGHRDQMAAARGI
          .ADVYKLL.QLKVVEDGILKLRNAGNEQDLGIQ.KALKPEV.KLNIMAAKRQQELKDVGHRDQMAAARGI
Retrocopy RADVYKLLIQLKVVEDGILKLRNAGNEQDLGIQNKALKPEVNKLNIMAAKRQQELKDVGHRDQMAAARGI

Parental  LQK-NVPILYTASQACLQHPDVAAYKANRDLIYKQLQQAVTGISNAAQ-ATASDDASQHQGGGGGELAYA
          L.K.NVPILYTASQACLQH.DVAAYKANRDLIYKQLQQAVTGISNAAQ.ATAS..ASQHQGGGGG.LAY.
Retrocopy L*K<NVPILYTASQACLQHHDVAAYKANRDLIYKQLQQAVTGISNAAQ<ATASGNASQHQGGGGGKLAYV

Parental  LNNFDKQIIVDPLSFSEERFRPSLEERLESIISGAALMADSSCTRDDRRERIVAECNAVRQALQDLLSEY
          LNNFDKQII....SFSE..FR.SLE..LESIISGAALM..SSCTRDD.....VAECNA.RQALQDLLSEY
Retrocopy LNNFDKQII---RSFSEKHFRSSLEACLESIISGAALMVESSCTRDDQSGPMVAECNAIRQALQDLLSEY

Parental  MGNAGRKERSDALNSAIDK-MTKKTRDLRRQLRKAVMDHVSDSFLETNVPLLVLIEAAKNGNEKEVKEYA
          .GNAG.KE.SD.LNSAIDK.MTKKTRDLRR.L.KAV.DH.SDS.LETNVPLLVL..AAKNGNEKEVKEYA
Retrocopy TGNAGPKEISDELNSAIDK<MTKKTRDLRRLLHKAVTDHISDSSLETNVPLLVLTGAAKNGNEKEVKEYA

Parental  QVFREHANKLIEV-ANLACSISNNEEGVKLVRMSASQLEALCPQVINAALALAAKPQ-SKLAQENMDLFK
          QVF.E.ANKLIEV.ANLA.SISNNEEG.KLV.MSASQ.EA.CPQVINAALALAAKP.......ENMDL.K
Retrocopy QVFHEQANKLIEV<ANLARSISNNEEGIKLVHMSASQSEAVCPQVINAALALAAKPE<VNWPKENMDLLK

Parental  EQWEKQVRVLTDAVDDITSIDDF-LAVSENHILEDVNKCVIALQEKDVDGL-DRTAGAIRGRAARVIHVV
          EQWEK.V.VLTDA.DDITSI.DF.L.VSENH.LEDVNKC..AL.EKDVDG..D.TAGAI.G.AARVIHVV
Retrocopy EQWEK*VHVLTDAIDDITSINDF<LVVSENHGLEDVNKCAFAL*EKDVDGR<DHTAGAI*GWAARVIHVV

Parental  TSEMDNYE
          TSE.DNYE
Retrocopy TSEIDNYE

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_516 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
Callithrix jacchus	ENSCJAG00000006820	1 retrocopy	retro_cjac_963,
Myotis lucifugus	ENSMLUG00000012995	1 retrocopy	retro_mluc_422,
Otolemur garnettii	ENSOGAG00000011865	1 retrocopy	retro_ogar_516 ,