RetrogeneDB ID: retro_cjac_2875

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:49871825..49873014(+)
• Located in intron of: ENSCJAG00000008645

Retrocopy information

• Ensembl ID: ENSCJAG00000008654
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSCJAG00000007877
• Aliases: None
• Description: Obg-like ATPase 1 [Source:HGNC Symbol;Acc:28833]

Sequence

>retro_cjac_2875
ATGCCCCCCAAGAAGGGAGGTGATGGAATTAAACCACCCCCAATCATTGGAAGATTTGGAACCTCACTGAAAATTGGTAT
TGTTGGATTGCCAAATGTTGGGAAATCTACTTTCTTCAATGTATTAACCAATAGTCAGGCTTCAGCAGAAAACTTCCCAT
TCTGCACTATTGATCCTAATGAGAGCAGAGTACCTGTGCCAGATGAAAGATTTGACTTTCTTTGTCAGTACCACAAACCA
GCAAGCAAAATTCCTGCCTTTCTAAATGTAGTGGATATTGCTGGCCTTGTGAAAGGAGCTCACAATGGGCAGGGCCTGGG
GAATGCTTTTTTATCTCATATTAGGTGCCTGTGATGGCATCTTTCACCTAACACGTGCTTTTGAAGATGATGATATCACG
CATGTTGAAGGAAGTGTAGATCCTATTCGAGATATAGAAACAATACATGAAGAGCTTCAGCTTAAAGATGAGGAAATGAT
TGGGCCCATTATAGATAAACTAGAAAAGGTGGCTGTGAGAGGAGGAGATAAAAAACTAAAACCTGAATATGATATAATGT
GCAAAGTAAAATCCTGGGTTATAGATCAAAAGAAACCTGTTTGCTTCTATCATGATTGGAATGACAAAGAGATTGAAGTG
TTGAATAAACACTTATTTTTGACTTCCAAACCAATGGTCTACTTGGTTAATCTTTCTGAAAAAGACTACATTCGAAAGAA
AAACAAATGGTTGATAAAAATTAAAGAGTGGGTGGACAAGTATGACCCAGGCGCCTTGGTCATTCCTTTTAGTGGGGCCT
TGGAACTCAAGTTGCAAGAATTGAGTGCTGAGAAGAGACAGAAGTATCTGGAAGCGAACATGACACAAAGTGCTTTGCCA
AAGATCATTAAGGCTGGATTTGCAGCACTCCAGCTAGAATACTTTTTCACTGCAGGCCCAGATGAAGTGCGTGCATGGAC
CATCAGGAAAGGGACTAAGGCTCCTCAGGCTGCAGGAAAGATCCACACAGATTTTGAAAAGGGATTCATTATGGCTGAAG
TAATGAAATATGAAGATTTTAAAGAGGAAGGTTCTGAAAATGCAGTCAAGGCTGCTGGAAAATACAGACAACAAGGCAGA
AATTATATTGTTGAAGATGGAGATATTATCTTCTTCAAATTTAACACACCTCAACAACCGAAGAAGAAA

Alignment

ORF - retro_cjac_2875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
          MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER
Retrocopy MPPKKGGDGIKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDER

Parental  FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHI-SACDGIFHLTRAFEDDDITHVEGSV
          FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHI..ACDGIFHLTRAFEDDDITHVEGSV
Retrocopy FDFLCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLSHI>GACDGIFHLTRAFEDDDITHVEGSV

Parental  DPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVRFYHDWNDK
          DPIRDIE.IHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPV.FYHDWNDK
Retrocopy DPIRDIETIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKPEYDIMCKVKSWVIDQKKPVCFYHDWNDK

Parental  EIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEER
          EIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAE.R
Retrocopy EIEVLNKHLFLTSKPMVYLVNLSEKDYIRKKNKWLIKIKEWVDKYDPGALVIPFSGALELKLQELSAEKR

Parental  QKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMK
          QKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMK
Retrocopy QKYLEANMTQSALPKIIKAGFAALQLEYFFTAGPDEVRAWTIRKGTKAPQAAGKIHTDFEKGFIMAEVMK

Parental  YEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
          YEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
Retrocopy YEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK

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	0.35 RPM	23.27 RPM
SRP051959_heart	0.25 RPM	17.52 RPM
SRP051959_kidney	0.47 RPM	24.18 RPM
SRP051959_liver	0.43 RPM	20.45 RPM
SRP051959_lung	0.33 RPM	12.72 RPM
SRP051959_lymph_node	0.16 RPM	14.04 RPM
SRP051959_skeletal_muscle	0.39 RPM	26.86 RPM
SRP051959_spleen	0.23 RPM	14.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2875 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2875 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875 ,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,