RetrogeneDB ID: retro_cjac_1235

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:83630184..83632022(+)
• Located in intron of: ENSCJAG00000008027

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSCJAG00000021574
• Aliases: None
• Description: Oxysterol-binding protein [Source:UniProtKB/TrEMBL;Acc:F6TIP2]

Sequence

>retro_cjac_1235
GGTTTGGATTCAGGATTTATTCCTAGTGCCCTAGACTTTGACAAAAAACTTACAGAAGCTGATGCTTACCTTCAAATCTT
GATTGAACAATTAAAACTTTTTGATGACAAGCTTCAAAACTGCAAAGAAGATGAACAAAGAAAGAAAATTGAAATGCTCA
AAGAGACAACGAACAGCATGGTAGAATCAATTAAACACTGAGTTGTGTTGCTGCAGATTGCTAAAAGTACTATTAATCCT
GTAGATGCAATATATCAACCTAGTCCTTTGGAACCTGTGGTCAGCACAATGCCTTCCCAGACTGTATTATCTCCAGAACC
TGTTCAGTTGTGTAAGTCAGAGCAATGTCCATCTTCCCTACCAGTTGGACCTATGTTGGCTACCTTGGTACATCATCAGA
CTCCTACACCAAATAGTACAGGCAGTGGCCATTCACCACCAAGTAGCAGTCTAACTTCTCCAAGCCATGTGAACTTGTCT
CCAAATACAGTCCCAGAGTTCTCTTACTCTAGCAGTGAAGATGAATTTTATGATGCCAACAAATTCCATCAAAGTGGCTC
ATCCCCAAAGCGCTTAATAGATTCTTCTGGATCTGCCTCAGTCCTGACACACAGCAGCTCAGGAAATAGTCTAAAACACC
CAGATACCACAGAATCACTTAATTCTTCCATGTCCAATGGAACAACCTTTTCGATTCACATGACGATAGAGATGATGATG
CGGAGGCAGGGTCCGTGGAGGAGCACAAGAGCGTTATTAGGTATCTCTTATCACAGGTTAGGCTTGGGATAGATCTTACT
AAGGTAGTTCTTCCAACATTTCTTCTTGAAAGAAGATCTCTTTTAGAAATGTATGCAGACTTTTTTGCACATTCGGACCG
GTTTGTGAGCATTAGTGACCACAAGTATCCCAAGGATCGAATGGTTCAGGTTGTGAAATGGTACCTCTCAGCCTTTCATG
CAGGAAGGAAAGGATCAGTTGCCAAAAAGCCATACAATCCCATTTTGGGCGAGATCTTTCAGTGTCATTGGATATTACCA
AATGATACAGAAGAGAACACAGAACTAGTTTCAGAAGGACCAGTTCCCTGGGTTTCCAAAAACAGTGTAACATTCGTGGC
TGAGCAGGTTTCCCATCATCCACCCATTTCAGCCTTTTATGCTGAGTGTTTTAACAAGAAGATACAATTCAATGCTCATA
TCTGAACCAAATCAAAATTCCTTGGGATGTCAATTGGGGTGCACAACATAGGGCAGGGCTGTGTCTCATGTCTTGACTAT
GATGAACATTACATTCTCACATTCCCCAATGGCTATGGAAGGTCTATCCTCACAGTGCCCTGGGTGGAATTAGGAGGAGA
ATGCAATATTAATTGTTCCAAAACAGGCTATAGTGTAAATATCTTCCACACTAAACCCTTCTATGGGGGCAAGAAGCACA
GAATTACTGCTGAGATTTTTTCTCCAAATGACAATAAGTCTTTTTGCTCAATTGAAGGGGAATGGAGTGGTGTGATGTAG
GCAAAATATGCAACAGGGGAAAATACAGTCTTTGTAGATACCAAGAAGTTGCCTATAATCAAGAAGAAAGTGAGGAAGTT
GGAAGATCAGAACGAGTATGAATCCCGCAGCCTTTGGAAGGATGTCACTTTCAACTTAAAAATCAGAGACATTGATGCAG
CAACTGAAGCAAAGCACAGGCTTGAAGAAAGACAAAGAGCAGAAGCCCGAGAAAGGAAGGAAAAGGAAATTCAGTGGGAG
ACAAGGTTATTTCATGAAGATGGAGAATGTTGGGTTTATGATGAACCATTACTGAAACGTCTTGGTGCTGCCATGCAT

Alignment

ORF - retro_cjac_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 94.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLDSGFIPSVQDFDKKLTEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIETLKETTNSMVESIKHCIVL
          GLDSGFIPS..DFDKKLTEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIE.LKETTNSMVESIKH..VL
Retrocopy GLDSGFIPSALDFDKKLTEADAYLQILIEQLKLFDDKLQNCKEDEQRKKIEMLKETTNSMVESIKH*VVL

Parental  LQIAKSTINPVDAIYQPSPLEPVVSTMPSQTVLPPEPVQLCKSEQRPSSLPVGPVLATLGPHQTPTPNST
          LQIAKSTINPVDAIYQPSPLEPVVSTMPSQTVL.PEPVQLCKSEQ.PSSLPVGP.LATL..HQTPTPNST
Retrocopy LQIAKSTINPVDAIYQPSPLEPVVSTMPSQTVLSPEPVQLCKSEQCPSSLPVGPMLATLVHHQTPTPNST

Parental  GSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDADEFHQSGSSPKRLIDSSGSASVLTHSSSGNS
          GSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDA..FHQSGSSPKRLIDSSGSASVLTHSSSGNS
Retrocopy GSGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDANKFHQSGSSPKRLIDSSGSASVLTHSSSGNS

Parental  LKRPDTTESLNSSMSNGTSDA-DLFDSHDDRDDDAEAGSVEEHKSVIMHLLSQVRLGMDLTKVVLPTFIL
          LK.PDTTESLNSSMSNGT....D..D..DD...DAEAGSVEEHKSVI..LLSQVRLG.DLTKVVLPTF.L
Retrocopy LKHPDTTESLNSSMSNGTTFS<DSHDDRDD---DAEAGSVEEHKSVIRYLLSQVRLGIDLTKVVLPTFLL

Parental  ERRSLLEMYADFFAHPDLFVSISDHKDPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQCHWTL
          ERRSLLEMYADFFAH.D.FVSISDHK.PKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQCHW.L
Retrocopy ERRSLLEMYADFFAHSDRFVSISDHKYPKDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQCHWIL

Parental  PNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMSIGVHN
          PNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHI.TKSKFLGMSIGVHN
Retrocopy PNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHI*TKSKFLGMSIGVHN

Parental  IGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIIFHTKPFYGGKKHRITAE
          IGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYS.N.IFHTKPFYGGKKHRITAE
Retrocopy IGQGCVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSVN-IFHTKPFYGGKKHRITAE

Parental  IFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRSLWKDVTFNLKI
          IFSPND.KSFCSIEGEW.GVM.AKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRSLWKDVTFNLKI
Retrocopy IFSPNDNKSFCSIEGEWSGVM*AKYATGENTVFVDTKKLPIIKKKVRKLEDQNEYESRSLWKDVTFNLKI

Parental  RDIEAATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAAKH
          RDI.AATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAA.H
Retrocopy RDIDAATEAKHRLEERQRAEARERKEKEIQWETRLFHEDGECWVYDEPLLKRLGAAMH

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	0.20 RPM	42.82 RPM
SRP051959_heart	0.32 RPM	61.88 RPM
SRP051959_kidney	0.13 RPM	92.16 RPM
SRP051959_liver	0.11 RPM	40.05 RPM
SRP051959_lung	0.34 RPM	68.53 RPM
SRP051959_lymph_node	0.80 RPM	64.65 RPM
SRP051959_skeletal_muscle	0.17 RPM	27.58 RPM
SRP051959_spleen	0.32 RPM	69.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1235 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021574	1 retrocopy	retro_cjac_1235 ,
Felis catus	ENSFCAG00000010298	1 retrocopy	retro_fcat_1134,
Gorilla gorilla	ENSGGOG00000004787	1 retrocopy	retro_ggor_737,
Microcebus murinus	ENSMICG00000002731	1 retrocopy	retro_mmur_1035,
Myotis lucifugus	ENSMLUG00000009199	1 retrocopy	retro_mluc_2149,
Nomascus leucogenys	ENSNLEG00000016138	2 retrocopies	retro_nleu_1820, retro_nleu_279,
Oryctolagus cuniculus	ENSOCUG00000004303	1 retrocopy	retro_ocun_281,
Pongo abelii	ENSPPYG00000001358	2 retrocopies	retro_pabe_689, retro_pabe_787,
Pan troglodytes	ENSPTRG00000000730	1 retrocopy	retro_ptro_632,
Ictidomys tridecemlineatus	ENSSTOG00000000692	1 retrocopy	retro_itri_1537,