RetrogeneDB ID: retro_cjac_1488

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:94274931..94276022(+)
• Located in intron of: None

Retrocopy information

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

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_1488
ATATTGGGTCTTGTGGGTCGTGTGGCCGCTACCTCCGCCTGCGGGGCCTTGCGGGGACTGAGCCCTTCAGCGTTGCTACC
CCCAGCGCAGCTCTTACTGCGGGCCACTCCAACAGCTGTCTATCCTGTCAGGGACTATGCGGCGCAAACATCTCCTTCGC
AAAGGCAGGCGCTGCCACCGGGCGCATCATGGCAGTCATTGGCGCAGTGGTGGACGTCCAGTTTGATGAGGGCCTACCAC
CCATCCTAAATGCCCTGGAAGTGCAAGGCAGGGAGACCAGACTGGTTTTGGAGGTGGCCCAGCATTTGGGTGAGAGCACA
GTAAGGACCATTGCTATAGATGGTACAGAGGGCTTGGTTAGAGGCCAGAAAGTACTGGATTCTGGTGCACCAATCAAAAT
TCCTGTTGGTCCTGAGACTTTGAGCAGAATCCTGAATGTCATTGGAGAACCTATTGATGAAAGAGGTCCCATCAAAACCA
AACAATTTGCTCCCATTCATGCTGAGGCTCCTGAATTAATGGAAATGAGTGTTGAGCAGGAAATTCTGGTGACTGGTATC
AAGGTTGTGGATCTGCTAGCTCCCTATGCCAAGGGTGGCAAAATTGGACTTTTTGGTGGTGCTGGAGTTGGCAAGACTGT
ACTGATCATGCAGTTAATCAACAATGTTGCCAAAGCCCATGGTGGTTACTCTGTGTTTGCTGGTGTTGGTGAGAGGACCC
ATGAAAGCAATGATTTATACCATGAAATGATTGAGTCTGGTGTTATCAACTTAAAAGATGCCACGTCTAAGGTAGCCCTG
GTATATGGTCAAATGAATGAACCACCTGGTGCTCGTGCCCGGGTAGCTCTGACTGGACTGACTGTGGCTGAATACTTCAG
AGACCAGGAAGGTCAGGATGTATTGCTATTTATGGATAACATCTTCTGCTTCACCCAGGCTGGTTCAGAGGTGTCTGCCT
TAATGGGCAGAATCCCTTCTGCTGTGGGCTATCAGCCTACCCTGGCCACTGACATGGGTACTATGCAGGAAAGAATTACC
ACCACCAAGAAGGGATCTATCACTTCTGTACAGGCCATCTATGTGCCTGCT

Alignment

ORF - retro_cjac_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.75 %
• Parental protein coverage: 68.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLGLVGRVAATSASGALRGLSPSASLPPAQLLLRATPTAVYPVRDYAAQTSPSP-KAGAATGRIVAVIGA
          .LGLVGRVAATSA.GALRGLSPSA.LPPAQLLLRATPTAVYPVRDYAAQTSPS..KAGAATGRI.AVIGA
Retrocopy ILGLVGRVAATSACGALRGLSPSALLPPAQLLLRATPTAVYPVRDYAAQTSPSQ<KAGAATGRIMAVIGA

Parental  VVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAMDGTEGLVRGQKVLDSGAPIKIPVGPE
          VVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIA.DGTEGLVRGQKVLDSGAPIKIPVGPE
Retrocopy VVDVQFDEGLPPILNALEVQGRETRLVLEVAQHLGESTVRTIAIDGTEGLVRGQKVLDSGAPIKIPVGPE

Parental  TLGRIMNVIGEPIDERGPIKTKQFAPIHAEAPEFMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAG
          TL.RI.NVIGEPIDERGPIKTKQFAPIHAEAPE.MEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAG
Retrocopy TLSRILNVIGEPIDERGPIKTKQFAPIHAEAPELMEMSVEQEILVTGIKVVDLLAPYAKGGKIGLFGGAG

Parental  VGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVSTGLIDVHMVVMPG
          VGKTVLIM.LINNVAKAHGGYSVFAGVGERT.E.NDLYHEMIESGVINLKDATSKV...L....M...PG
Retrocopy VGKTVLIMQLINNVAKAHGGYSVFAGVGERTHESNDLYHEMIESGVINLKDATSKVA--LVYGQMNEPPG

Parental  NYCQLKPCLLTLNSISKPPRLAQVFFLVDSPLIFGRGGLDVDLYLSNIRSCLFGQERWLTPVIAVLNPIS
          .........LT............V....D....F...G..V......I.S....Q....T........I.
Retrocopy ARARVALTGLTVAEYFRDQEGQDVLLFMDNIFCFTQAGSEVSALMGRIPSAVGYQPTLATDMGTMQERIT

Parental  TENTKNVISVHAIYVPA
          T.......SV.AIYVPA
Retrocopy TTKKGSITSVQAIYVPA

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	1.44 RPM	107.50 RPM
SRP051959_heart	2.09 RPM	246.72 RPM
SRP051959_kidney	2.33 RPM	142.35 RPM
SRP051959_liver	1.67 RPM	148.64 RPM
SRP051959_lung	1.37 RPM	45.04 RPM
SRP051959_lymph_node	1.89 RPM	51.50 RPM
SRP051959_skeletal_muscle	1.70 RPM	312.72 RPM
SRP051959_spleen	1.20 RPM	50.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1488 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1488 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,