RetrogeneDB ID: retro_cjac_588

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:91330873..91333744(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRBD1
• Ensembl ID: ENSCJAG00000000727
• Aliases: None
• Description: None

Sequence

>retro_cjac_588
ATGTCATCACTGCCAAGAAGAGCAAAAGTACAGGTCCAGGGTGTGGCATCAAAAGATGAATTTTCTTCATTCTCTGAGTT
ATCATCTGCCTCTGAAGAAGATGACAAGGAAGATAGTTCCTGGGATCCCCAAAAGAAAGTTTCCAGAAGCTGTAAACAGC
TCGTTCCCAAGGAATCCAAACCAATGAGGATGCCTCGGGTGAAGAAGAATACCCCATAGATCAGTGATGACTCAGAAGTT
GTTAAGGAGGAGCTGAATAGCCCTGTGGCTGTTGCTGATACTGCTTTGGAAGATAGAAAAAATAAATTGGATACTGTAGA
GACTCTGAAAACAGCCAAGACAAAATGGAAATGTTCAGCGCAGCCACATTCAGCTCAGAGGACCAAAAAGCTGAAAGTTG
AAGGAGAAACCAGCAAAGCCACCAACTTAGAGGGTGAGAGTAATAGTTCAGAGACACCATCCAGAAGCACTATATGCGGA
GGTACCTGCAAGAAGGAAGAGAATGAAGATGACTTTACATTTGGTCAGTCCCCTTTAAAGAAAATGAAGACTGAAACATG
TCCTCAGGGACAGCCTGTCAAGTTTCCAGCAAATGCCATAATACTAAAGAGGAGGTGGAAATGAATTGGGACATAGTACA
GGTTTTATCTGAAAGAACTAATGTTGAACCTTGGGTTTGTGCCAACGCCATTCGTCTCCTTAATGATGATAACACAATTC
CCTTCATTATATGTTATCAAAAAGAGCTCATTAAAAACCTTGATGCTGATTCCTTGAGAGAAGTTCAACAAACCCTAGAA
GAACTACGAGCCATTGTAAAGAAAGTTCATAATACAATCCAGAAAATTAAGAAGGAAGGGAAGATGTCTGAGTGCTTCTT
AAAAGCCTTGCTGAATTGTAAAACATTTGAAGAACTAGAACATGTGTCTGCTTCATATAAAACAAAGGGCAAAGGGACCA
AAGCCCAGAGAGCAAGACAGTTGGGCTTAGAAGGAGCAGCCAGGACACTGCTTGAGAAACCAGGGGAGCTTAATCTGCTA
TCATACATTAGGCCTGATGTTAAAGGGCTTTCAGCGCTCCAGGATATTGAAACAGGAGTGCAGCATATTTTAGCAGACAT
GATTGCTAAAGACAAAGATGCTTGACTTCATTCGGAACTTGTGCCAGAACAGACTTGTTTCTATCCAGTCGTCTCTGGCA
AAAGTGTCCTCAAAAAAGGTAAATGAGAAAGATGTTGATAAGTTTCTGCTGTATCAGCATTTTTCATGCAACATAAGAAC
CATTCACCATCATCAGATTCTTGCAATTAACCGTGGAGAAAATTTGAAGACACTGACGGTTAAGGTGGATATTTCTGATG
GAGTGAAGAATGAATTCTGTAGGTGGTGCATCCAAAACAGGTGGAGACCATGTAGCTTTGCAAGGCCAGAGGTAATGAAG
ATCTTACATAATTCATTAGATGATTCCTTTAAACGCCTTATTTATCCTCTCCTCTGTAGAGAATTCAGAGCCAAACTAAC
ATCAGATGCAGAGAAGGAATCAGTAATGATGTTTGGATGGAATCTTCGTCAGCTCCTTTTAACAAGCCCTGTTCCAGGGC
ACACCTTAATGGGAGTGGATCCTGGTTATAAACGTGGTTGCAAATTAGCTATAATTTCTCCTACCAGTAAGATACTTCAT
ACTGATGTGGTTTACCTGCATTGTGGACAAGGCTTCCGAGAGGCAGAGAAAATAAAGAGGCTTTTGCTGGATTTCAACTG
CAGCACAGTAGGGATTGGAAACGGAACTGCCTGCCAGGAGACAGAAGCTTACTTTGCTGACCTGATAATGAAAAATTATT
TTGCACCACTGGATGTTGTTTACTGTATCGTCAGTGAAGCAGGAGCATCAATCTACAGTGTCAGCCCTGAAGTTAGCAAA
GAGATGCCAGGGCTGGACCCTAATTTAAGAAGTGTAGTTTCCATAGCAAGGTGTGTACAAGATCCATTAGCTGAGCTAGT
GAAAATTGAGCCAAAGCACATTGGAGTTGGAATGTATCAGCATGATGTATCCCAGACTTTACTCAAGGCAACACTGGACA
GCATTGTAGAACAATGTGTCAGCTTTGTGGGAGTGGATATTAACATCTGTTCAGAAGTTTTGTTAAGGCATATTGCAGGA
CTCAATGCCAACAGAGCCAAAAATATTATTGAATGGCGAGAGAAAAATGGACCCTTTATCAACCGCGAACAGCTGAAGAA
AGTGAAGAGGCTGGGTCCAAAATTCTTCCAACAGTGTGCTGGCTTCATCAGAATCAACCAGGATTATATCCAAACATTTT
GCAGTCAGCAAACTGAATCTTCAGGCCAAATTCAAGGAGTTGCTGTGACATCTTTAGCAGATGTTGAGGTCACAAATGAG
AAGCAGGGCAAAAAGAAGAGCAAAACTGCAGTGAATGTTTTACTGAAGCCAAATCCTTTGGACCAAACTTGTATTCATCC
AGAATCATATGACATAGCAATGAGGTTTTTATCATCCATTGGAGGGACACTCTGTGAGATTGGAAAGCCTGAAATGCAAC
AAAAAATAAATTCATTTCTTGAGAAGGAAGGAATAGAGAAAACTGCAGAAAGATTGCAAACAACAGTACACACTTTACAG
GTCATCATAGATGGTCTCAGTCAGCCTGAAAGCTTTGACTTTTGAACAGATTTTGATAAACCTGATTTCAAGAGAAGCAT
AGTATGCCTGGAAGATCTGTAGGTTGGGACAGTTCTTACAGGCAGAGTTGAGAATGTCACTCTCTTTGGAATTTTTGTGG
ATATAGGAGTGAGGAAAGCTGGTCTAATTCCCATACGAAATGTAACAGAAGCAAAACTTTCAAAAACAAAG

Alignment

ORF - retro_cjac_588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.34 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSLPRRAKVQVQGVVSKDEFSSVSELSSASEEDDKEDSSWEPQKKASRSRKQLVPKESKPKRMPRVKKN
          MSSLPRRAKVQVQGV.SKDEFSS.SELSSASEEDDKEDSSW.PQKK.SRS.KQLVPKESKP.RMPRVKKN
Retrocopy MSSLPRRAKVQVQGVASKDEFSSFSELSSASEEDDKEDSSWDPQKKVSRSCKQLVPKESKPMRMPRVKKN

Parental  TPQISDDSEVVVKEELNSSVAAADTALEDRKNKLDTVETPKTAKTKRKCSAQPHSAQRTKKLKVDEETSK
          TP.ISDDSEVV.KEELNS.VA.ADTALEDRKNKLDTVET.KTAKTK.KCSAQPHSAQRTKKLKV..ETSK
Retrocopy TP*ISDDSEVV-KEELNSPVAVADTALEDRKNKLDTVETLKTAKTKWKCSAQPHSAQRTKKLKVEGETSK

Parental  ATNLEGESNSSETPSTSTICRGTCKKEENEDDFTFGQSPLKKMKTETCPQGQPVKFPANA-NNTKEEVEM
          ATNLEGESNSSETPS.STIC.GTCKKEENEDDFTFGQSPLKKMKTETCPQGQPVKFPANA..NTKEEVEM
Retrocopy ATNLEGESNSSETPSRSTICGGTCKKEENEDDFTFGQSPLKKMKTETCPQGQPVKFPANA<HNTKEEVEM

Parental  NWDIVQVLSERTNVEPWVCANAIRLFNDDNTIPFIIRYRKELINNLDADSLREVQQTLEELRAVVKKVHN
          NWDIVQVLSERTNVEPWVCANAIRL.NDDNTIPFII.Y.KELI.NLDADSLREVQQTLEELRA.VKKVHN
Retrocopy NWDIVQVLSERTNVEPWVCANAIRLLNDDNTIPFIICYQKELIKNLDADSLREVQQTLEELRAIVKKVHN

Parental  TIQKIKKEGKMSECLLKALLNCKTFEELEHVSAPYKTGSKGTKAQRARQLGLEGAARTLLEKPGELNLLS
          TIQKIKKEGKMSEC.LKALLNCKTFEELEHVSA.YKT..KGTKAQRARQLGLEGAARTLLEKPGELNLLS
Retrocopy TIQKIKKEGKMSECFLKALLNCKTFEELEHVSASYKTKGKGTKAQRARQLGLEGAARTLLEKPGELNLLS

Parental  YIRPDVKGLSTLRDIETGVQHILADMIA-KDKDTLDFIRNLCQNRHVSIQSSLAKVSSKKVNEKDVDKFL
          YIRPDVKGLS.L.DIETGVQHILADMIA.K.K..LDFIRNLCQNR.VSIQSSLAKVSSKKVNEKDVDKFL
Retrocopy YIRPDVKGLSALQDIETGVQHILADMIA>KTK-MLDFIRNLCQNRLVSIQSSLAKVSSKKVNEKDVDKFL

Parental  LYQHFSCNIRTIHHHQILAINRGENLKILTVKVDISDGVKNEFCRWCIQNRWRPRSFARPEVMKILHNSL
          LYQHFSCNIRTIHHHQILAINRGENLK.LTVKVDISDGVKNEFCRWCIQNRWRP.SFARPEVMKILHNSL
Retrocopy LYQHFSCNIRTIHHHQILAINRGENLKTLTVKVDISDGVKNEFCRWCIQNRWRPCSFARPEVMKILHNSL

Parental  DDSFKRLIYPLLCREFRAKLTSDAEKESVMMFGRNLRQLLLTSPVPGRTLMGVDPGYKHGCKLAIISPTS
          DDSFKRLIYPLLCREFRAKLTSDAEKESVMMFG.NLRQLLLTSPVPG.TLMGVDPGYK.GCKLAIISPTS
Retrocopy DDSFKRLIYPLLCREFRAKLTSDAEKESVMMFGWNLRQLLLTSPVPGHTLMGVDPGYKRGCKLAIISPTS

Parental  QILHTDVVYLHCGQGFREAEKIKRLLLNFNCSTVVIGNGTACRETEAYFADLIMKNYFAPLDVVYCIVSE
          .ILHTDVVYLHCGQGFREAEKIKRLLL.FNCSTV.IGNGTAC.ETEAYFADLIMKNYFAPLDVVYCIVSE
Retrocopy KILHTDVVYLHCGQGFREAEKIKRLLLDFNCSTVGIGNGTACQETEAYFADLIMKNYFAPLDVVYCIVSE

Parental  AGASIYSVSPEASKEMPGLDPNLRSAVSIARRVQDPLAELVKIEPKHIGVGMYQHDVSQTLLKATLDSVV
          AGASIYSVSPE.SKEMPGLDPNLRS.VSIAR.VQDPLAELVKIEPKHIGVGMYQHDVSQTLLKATLDS.V
Retrocopy AGASIYSVSPEVSKEMPGLDPNLRSVVSIARCVQDPLAELVKIEPKHIGVGMYQHDVSQTLLKATLDSIV

Parental  EECVSFVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKGLGPKSFQQCAGFIRIN
          E.CVSFVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVK.LGPK.FQQCAGFIRIN
Retrocopy EQCVSFVGVDINICSEVLLRHIAGLNANRAKNIIEWREKNGPFINREQLKKVKRLGPKFFQQCAGFIRIN

Parental  QDYIRTFCSQQTESSGQIQGVTVTSLAEVEVTNQKQGKKKSKTAVNVLLKPNPLDQTCIHPESYDIAMRF
          QDYI.TFCSQQTESSGQIQGV.VTSLA.VEVTN.KQGKKKSKTAVNVLLKPNPLDQTCIHPESYDIAMRF
Retrocopy QDYIQTFCSQQTESSGQIQGVAVTSLADVEVTNEKQGKKKSKTAVNVLLKPNPLDQTCIHPESYDIAMRF

Parental  LSSIGGTLFEIGRPEIQQKIISFLEKEGIEKAAERLQTTVHTLQVIIDGLRQPESFDFRTDFDKPDFKRS
          LSSIGGTL.EIG.PE.QQKI.SFLEKEGIEK.AERLQTTVHTLQVIIDGL.QPESFDF.TDFDKPDFKRS
Retrocopy LSSIGGTLCEIGKPEMQQKINSFLEKEGIEKTAERLQTTVHTLQVIIDGLSQPESFDF*TDFDKPDFKRS

Parental  IVCLEDLQVGTVLTGRVENATLFGIFVDIGVGKAGLIPIRNVTEAKLSKTK
          IVCLEDL.VGTVLTGRVEN.TLFGIFVDIGV.KAGLIPIRNVTEAKLSKTK
Retrocopy IVCLEDL*VGTVLTGRVENVTLFGIFVDIGVRKAGLIPIRNVTEAKLSKTK

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
SRP051959_colon	0.11 RPM	21.26 RPM
SRP051959_heart	0.04 RPM	15.91 RPM
SRP051959_kidney	0.07 RPM	16.66 RPM
SRP051959_liver	0.04 RPM	16.74 RPM
SRP051959_lung	0.08 RPM	22.14 RPM
SRP051959_lymph_node	0.07 RPM	25.94 RPM
SRP051959_skeletal_muscle	0.04 RPM	8.95 RPM
SRP051959_spleen	0.08 RPM	26.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_588 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_588 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_588 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000727	1 retrocopy	retro_cjac_588 ,