RetrogeneDB ID: retro_cjac_543

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:71046589..71047979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPOLA
• Ensembl ID: ENSCJAG00000006512
• Aliases: None
• Description: None

Sequence

>retro_cjac_543
ATTACAACACAGGGATCACAACAAACACAACCACCACACAAGCACTATGGCATCACTTCTCCTATCAGCTTAGCAGCCCC
CAAGGAGACTAACTGCATACTTACACAGAAACTAATTGAGACACTGAAACCCTTCAGGGTTTTTGATGAGGAAGAGGAAC
TGCAGCGCAGGATTCTAATTTTGGGAAAACTAACCTGGTAAAAAAGTGGATACGAGAAATCAATGAAAGCAAGAATCTTC
AATTACAGTCTGTAATTGAAAATATTGGAGGACAAATTTTTACATTTGGATCTTACGGTTAGGCGTACATACAGAAGGTG
CTGAATTGGATGCGTTGTGTGTTGCACCAAGACATGTTGATCGAGGTGACTTTTTCACCTCATTCTATGATGAGTTGAAA
TTACAGGAAGAAGTAAAAGATTTAAGAGCTGTTGAAGAGGCATTCATACCAGTTATTAAACTCTGTTTTGATGGGATAGA
GATGGATATTTTGTTTGCAAGATTAGCACTGCCGACAATTCCAGAAGATTTGGACCTACGAGATGACAGTCTGCTTAAAA
ATTTAGATATAAGATGTATTAAGAAGTCTTAACGGTTGCAGGGTAACCGATGAAATTTTACATCTAGTACCAAACATTGA
CAACTTCAGGTTAACTATGAGAGCTAACAAACTGTGGGCCAAACGCCACAACATCTATTCCAATATATTAGGTTTCCTCA
GTGGTGTTTCCTGGGCTATGCTAGTAGCAAGAACTTGCCAGCTTTATCCAAATGCAATAGCATCAACACTTGTACATAAA
TTTTTCTTGGTATTTTCTAAATGGGAATGGCCAAATCCCGTGCTATTGAAACAGCCTGAAGAATGCAATCTTAATTTGCC
TGTATGGGACCCAAGGGTAAATCCCAGTGATAGGTACCATCTTATGCCTATAATTACACCAGCATACCGACAACAGAACT
CCACAGTACAACGTGTTCGTTTCAACATGGGTGGTCATGGTTGAGGAGTTTAAACGGGTTTTGCTATCACAGATGAAATT
TTGCTGAGTAAGGCAGAGTGGTCTAAACTTTTTGAAGCTCCAAACTTCTTTCAAAAGTACAGGCATTATATTGTACTTCT
AGCAAGTGCACCAACAGAAAAACAACACCTAGAATGGGCGGGCTTGGTGGAATCAAGAATCTGAATCCTAGTTGGAAGCT
TGGAGAAGATTGAATTTATTACACTGGTGCATGTGAATCCCCAGTCATTTCCAGCACCCAAAGAAAATCCTGACAAGGAA
GAATTTCACACGATGTGGGTGATTGGGTCAGTGTTTAAAAAACAGAAAACTCTGAAAACCTCAGTTTTGATCTCACCTAT
GATATTCAGTCTTTCACAGATACAGTTTTT

Alignment

ORF - retro_cjac_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.02 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VTTQGSQQTQPPQKHYGITSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILIL-GKLNNLVK
          .TTQGSQQTQPP.KHYGITSPISLAAPKET.CILTQKLIETLKPF.VF.EEEELQRRILIL.GK..NLVK
Retrocopy ITTQGSQQTQPPHKHYGITSPISLAAPKETNCILTQKLIETLKPFRVFDEEEELQRRILIL<GK-TNLVK

Parental  EWIREISESKNLP-QSVIENVGGKIFTFGSY-RLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQE
          .WIREI.ESKNL..QSVIEN.GG.IFTFGSY.RLGVHT.GA..DALCVAPRHVDR.DFFTSFYD.LKLQE
Retrocopy KWIREINESKNLQLQSVIENIGGQIFTFGSY<RLGVHTEGAELDALCVAPRHVDRGDFFTSFYDELKLQE

Parental  EVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCI-RSLNGCRVTDEI
          EVKDLRAVEEAF.PVIKLCFDGIE.DILFARLAL.TIPEDLDLRDDSLLKNLDIRCI.RSLNGCRVTDEI
Retrocopy EVKDLRAVEEAFIPVIKLCFDGIEMDILFARLALPTIPEDLDLRDDSLLKNLDIRCI>RSLNGCRVTDEI

Parental  LHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
          LHLVPNIDNFRLT.RA.KLWAKRHNIYSNILGFL.GVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
Retrocopy LHLVPNIDNFRLTMRANKLWAKRHNIYSNILGFLSGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE

Parental  WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNST-YNVSVSTRMVMVEEFKQ-GLAIT
          WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAY.QQNST.YNV.VST..VMVEEFK..G.AIT
Retrocopy WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYRQQNST>YNVFVSTWVVMVEEFKR<GFAIT

Parental  DEILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNP
          DEILLSKAEWSKLFEAPNFFQKY.HYIVLLASAPTEKQ.LEW.GLVES.I.ILVGSLEK.EFITL.HVNP
Retrocopy DEILLSKAEWSKLFEAPNFFQKYRHYIVLLASAPTEKQHLEWAGLVESRI*ILVGSLEKIEFITLVHVNP

Parental  QSFPAPKENPDKEEFRTMWVIGLVFK-KTENSENLSVDLTYDIQSFTDTVY
          QSFPAPKENPDKEEF.TMWVIG.VFK.KTENSENLS.DLTYDIQSFTDTV.
Retrocopy QSFPAPKENPDKEEFHTMWVIGSVFK<KTENSENLSFDLTYDIQSFTDTVF

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	0.00 RPM	99.18 RPM
SRP051959_heart	0.02 RPM	79.07 RPM
SRP051959_kidney	0.07 RPM	99.35 RPM
SRP051959_liver	0.02 RPM	87.49 RPM
SRP051959_lung	0.07 RPM	113.47 RPM
SRP051959_lymph_node	0.09 RPM	137.71 RPM
SRP051959_skeletal_muscle	0.04 RPM	58.79 RPM
SRP051959_spleen	0.00 RPM	114.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_543 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_543 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_543 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014142	1 retrocopy	retro_amel_517,
Bos taurus	ENSBTAG00000004054	1 retrocopy	retro_btau_1078,
Canis familiaris	ENSCAFG00000017783	1 retrocopy	retro_cfam_1783,
Callithrix jacchus	ENSCJAG00000006512	2 retrocopies	retro_cjac_1763, retro_cjac_543 ,
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Macaca mulatta	ENSMMUG00000018610	1 retrocopy	retro_mmul_1675,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mustela putorius furo	ENSMPUG00000003054	1 retrocopy	retro_mputfur_1375,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Nomascus leucogenys	ENSNLEG00000000625	1 retrocopy	retro_nleu_2771,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Pongo abelii	ENSPPYG00000006128	1 retrocopy	retro_pabe_3113,
Pan troglodytes	ENSPTRG00000006704	1 retrocopy	retro_ptro_2595,
Pteropus vampyrus	ENSPVAG00000013925	1 retrocopy	retro_pvam_360,
Vicugna pacos	ENSVPAG00000006464	1 retrocopy	retro_vpac_378,