RetrogeneDB ID: retro_cjac_928

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:81511995..81513582(-)
• Located in intron of: ENSCJAG00000007283

Retrocopy information

• Ensembl ID: ENSCJAG00000016499
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSCJAG00000033571
• Aliases: None
• Description: ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:F7E965]

Sequence

>retro_cjac_928
ATGTTGGGTCTTGTGGGTCGTGTGGCCGCTACCTCGGCCTCCGGGGCCTTGCGGGGACTGAGCCCTTCAGCGTCGCTACC
CCCAGTGCAGCTCTTACTGTGGGCCACTCCAACGGCGGTCTATCCTGTCAGGGACTATGCGGCTCAAACATCTCCTTCGC
CGAAGGCAGGCGCCGCTACCGGGCGCATCGTGGCGGTCATTGGCGCAGTGGTGGACGTCCAGTTTGATGAGGGACTACCA
CCGATCCTAAATGCCCTGGAAGTGCAAGGCAGGGAGACCAGACTGGTTTTGGAGGTGGCCCAGCATTTGGGTGAGAGCAC
AGTTAGGACCATTGCTATGGATGGTACAGAGGGCTTGGTTAGAGGCCAGAAAGTACTGGATTCTGGTGCACCAATCAAAA
TTCCTGTTGGTCCTGAGACTTTGGGCAGAATTATGAATGTCATTGGAGAACCTATTGATGAAAGAGGTCCCATCAAAACC
AAACAATTTGCTCCCATTCATACTGAGGCTCCTGAATTCATGGAAATGAATGTTGAGCAGGAAATTCTGGTGACTGGTAT
CAAGGTTGTGGATCTGCTAGCTCCCTATGCCAAGGGTGGCAAAATTGGGCTTTTTGGTGGTGCTGGAGTTGGCAAGACTG
TACTGATCATGGAGTTAATCAACAATGTTGCCAAAGCCCATGGTGGTTACTCTGTGTTTGCTGGTGTTGGTGAGAGAACC
CGTGAAGGCAATGATTTATACCATGAAATGATTGAGTCTGGTGTTATCAACTTAAAAGATGCCACCTCTAAGGTAGCCCT
GGTATATGGTCAAATGAATGAACCACCTGGTGCTCGTGCCCGGGTAGCTCTGACTGGACTGACTGTGGCTGAATACTTCA
GAGACCAGGAAGGTCAGGATGTATTGCTATTTATTGATAACATCTTCGGCTTCACCCAGGCTGGTTCAGAGGTGTCTGCC
TTATTGGGTAGAATCCCTTCTGCTGTAGGCTATCAGCCTACCCTGGCCACTGACATGGGTACTATGCAGGAAAGAATTAC
CACCACCAAGAAGGGATCTATCACTTCTGTACAGGCCATCTATGTGCCTGCTGATGACTTGACTGACCCTGCCCCTGCTA
CTACATTTGCCCATTTGGATGCTACCACTGTACTGTCCTGTGCCATTGCTGAGCTGGGCATCTATCCAGCTGTGGATCCT
CTGGACTCCACTTCTCGCATCATGGATCCCAACATTGTTGGCAGTGAGCATTACGATGTTGCCCGTGGGGTGCAAAAGAT
CCTGCAGGACTACAAATCCCTCCAGGATATCATTGCCATCCTGGGTATGGATAAACTTTCTGAGGAAGACAAGTTGACTG
TGTCCCATGCACGGAAAATACAGCGTTTCTTGTCTCAGCCATTCCAGGTTGCTGAGGTCTTCACAGGTCATATGGGGAAG
CTGGTACCCCTGAAGGAGACCATCAAAGGATTCCAGCAGATTTTGGCAGGTGAATATGACCATCTCCCAGAACAGGCCTT
CTATATGGTGGGACCCATTGAAGAAGCTGTGGCAAAAGCTGATAAGCTGGCTGAAGAGCATTCATCA

Alignment

ORF - retro_cjac_928 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLGLVGRVAATSASGALRGLSPSASLPPAQLLLRATPTAVYPVRDYAAQTSPSPKAGAATGRIVAVIGAV
          MLGLVGRVAATSASGALRGLSPSASLPP.QLLL.ATPTAVYPVRDYAAQTSPSPKAGAATGRIVAVIGAV
Retrocopy MLGLVGRVAATSASGALRGLSPSASLPPVQLLLWATPTAVYPVRDYAAQTSPSPKAGAATGRIVAVIGAV

Parental  VDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPET
          VDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPET
Retrocopy VDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPET

Parental  LGRIMNVIGEPIDERGPIKTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV
          LGRIMNVIGEPIDERGPIKTKQFAPIH.EAPEFMEM.VEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV
Retrocopy LGRIMNVIGEPIDERGPIKTKQFAPIHTEAPEFMEMNVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAGV

Parental  GKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVSTGLIDVHMVVMPGN
          GKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKV...L....M...PG.
Retrocopy GKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVA--LVYGQMNEPPGA

Parental  YCQLKPCLLTLNSISKPPRLAQVFFLVDSPLIFGRGGLDVDLYLSNIRSCLFGQERWLTPVIAVLNPIST
          ........LT............V....D....F...G..V...L..I.S....Q....T........I.T
Retrocopy RARVALTGLTVAEYFRDQEGQDVLLFIDNIFGFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITT

Parental  ENTKNVISVHAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIVGSEHY
          .......SV.AIYVPADDLTDPAPATTFAHLDATTVLS.AIAELGIYPAVDPLDSTSRIMDPNIVGSEHY
Retrocopy TKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSCAIAELGIYPAVDPLDSTSRIMDPNIVGSEHY

Parental  DVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQRFLSQPFQVAEVFTGHMGKLVPLKETI
          DVARGVQKILQDYKSLQDIIAILGMD.LSEEDKLTVS.ARKIQRFLSQPFQVAEVFTGHMGKLVPLKETI
Retrocopy DVARGVQKILQDYKSLQDIIAILGMDKLSEEDKLTVSHARKIQRFLSQPFQVAEVFTGHMGKLVPLKETI

Parental  KGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHSS
          KGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHSS
Retrocopy KGFQQILAGEYDHLPEQAFYMVGPIEEAVAKADKLAEEHSS

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	39.45 RPM	107.50 RPM
SRP051959_heart	97.17 RPM	246.72 RPM
SRP051959_kidney	58.08 RPM	142.35 RPM
SRP051959_liver	59.18 RPM	148.64 RPM
SRP051959_lung	18.98 RPM	45.04 RPM
SRP051959_lymph_node	18.65 RPM	51.50 RPM
SRP051959_skeletal_muscle	113.08 RPM	312.72 RPM
SRP051959_spleen	18.38 RPM	50.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_928 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_928 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928 ,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,