RetrogeneDB ID: retro_cjac_2541

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:84303126..84303450(+)
• Located in intron of: ENSCJAG00000001554

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001174
• Aliases: None
• Description: Cytochrome c oxidase subunit 6A, mitochondrial [Source:UniProtKB/TrEMBL;Acc:F7I4Z3]

Sequence

>retro_cjac_2541
ATGGCGGCAGCTGTTGCCTCTCGGCTTTCTTGGCTGCTGGGTTGGTCCCGCCCATAGCTGGGGCTGCCTATGTCGAGTGC
TGCCCATAGTGGAGAAGGTTCAGCTCTCATGTAGAAGGTCTTCACCTTCTTCGTCACGCTCCCTGGGGTGGGAGTCAGCA
TGCTGAATGTGTACCTGACGTTGCAAAAAGAGCATGAGACACCCGAGTTCGTCACCTACCCTCATCTCTGCATCAGGACC
AAGCCGTTTCCCTGGGGAGATGGTAACCAAACCCTATTCCATAACTCTCATGTGAATCCACTTCCAACTGGCTACGAAGA
TGAA

Alignment

ORF - retro_cjac_2541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVASRLSRLLGRSRPQVGRPMSSAAHSGEGSARMWKILTFFVALPGVGVSMLNVYLKSQKEHERPEF
          MAAAVASRLS.LLG.SRP..G.PMSSAAHSGEGSA.M.K..TFFV.LPGVGVSMLNVYL..QKEHE.PEF
Retrocopy MAAAVASRLSWLLGWSRP*LGLPMSSAAHSGEGSALM*KVFTFFVTLPGVGVSMLNVYLTLQKEHETPEF

Parental  VAYPHLRIRTKPFPWGDGNHTLFHNSHVNPLPTGYEDE
          V.YPHL.IRTKPFPWGDGN.TLFHNSHVNPLPTGYEDE
Retrocopy VTYPHLCIRTKPFPWGDGNQTLFHNSHVNPLPTGYEDE

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	0.31 RPM	34.39 RPM
SRP051959_heart	0.37 RPM	14.28 RPM
SRP051959_kidney	0.80 RPM	54.80 RPM
SRP051959_liver	0.35 RPM	59.59 RPM
SRP051959_lung	0.73 RPM	23.51 RPM
SRP051959_lymph_node	0.73 RPM	20.96 RPM
SRP051959_skeletal_muscle	0.28 RPM	6.33 RPM
SRP051959_spleen	0.84 RPM	28.28 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2541 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012788	1 retrocopy	retro_btau_229,
Canis familiaris	ENSCAFG00000031458	1 retrocopy	retro_cfam_506,
Choloepus hoffmanni	ENSCHOG00000009222	2 retrocopies	retro_chof_2085, retro_chof_2579,
Callithrix jacchus	ENSCJAG00000001174	6 retrocopies	retro_cjac_102, retro_cjac_1332, retro_cjac_205, retro_cjac_2541 , retro_cjac_3173, retro_cjac_912,
Cavia porcellus	ENSCPOG00000006426	1 retrocopy	retro_cpor_1265,
Equus caballus	ENSECAG00000012512	2 retrocopies	retro_ecab_578, retro_ecab_845,
Echinops telfairi	ENSETEG00000016826	1 retrocopy	retro_etel_1482,
Felis catus	ENSFCAG00000031188	9 retrocopies	retro_fcat_1049, retro_fcat_1399, retro_fcat_1505, retro_fcat_1518, retro_fcat_1653, retro_fcat_1891, retro_fcat_318, retro_fcat_753, retro_fcat_886,
Myotis lucifugus	ENSMLUG00000010330	4 retrocopies	retro_mluc_1127, retro_mluc_1405, retro_mluc_1879, retro_mluc_465,
Oryctolagus cuniculus	ENSOCUG00000009873	6 retrocopies	retro_ocun_1320, retro_ocun_1668, retro_ocun_1700, retro_ocun_174, retro_ocun_1898, retro_ocun_1928,
Otolemur garnettii	ENSOGAG00000003561	18 retrocopies	retro_ogar_1068, retro_ogar_111, retro_ogar_1150, retro_ogar_1466, retro_ogar_188, retro_ogar_1904, retro_ogar_2063, retro_ogar_2312, retro_ogar_2933, retro_ogar_3021, retro_ogar_3106, retro_ogar_3190, retro_ogar_3227, retro_ogar_3240, retro_ogar_346, retro_ogar_852, retro_ogar_871, retro_ogar_872,
Pteropus vampyrus	ENSPVAG00000002226	3 retrocopies	retro_pvam_1060, retro_pvam_790, retro_pvam_910,
Rattus norvegicus	ENSRNOG00000001170	2 retrocopies	retro_rnor_2581, retro_rnor_2680,
Tupaia belangeri	ENSTBEG00000008018	4 retrocopies	retro_tbel_2490, retro_tbel_3010, retro_tbel_3167, retro_tbel_395,
Tarsius syrichta	ENSTSYG00000011541	1 retrocopy	retro_tsyr_1025,
Tursiops truncatus	ENSTTRG00000000142	2 retrocopies	retro_ttru_1873, retro_ttru_889,
Vicugna pacos	ENSVPAG00000010359	1 retrocopy	retro_vpac_218,