RetrogeneDB ID: retro_cjac_113

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:51848698..51849154(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022908
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSCJAG00000011620
• Aliases: None
• Description: myosin, light chain 6B, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:29823]

Sequence

>retro_cjac_113
ATGTGTGACTTCACCAAAGACCAAACCACAGAGTTCAAGGAGGCCTTCCAGCTGTTTGACCGAACAGGTGATGGCAAGAT
CCTGTACAGCCAGTGTGGGGACGTGATGAGGGCCCTGGGCCAGAACCCCAACAACGCCGAGGTGCTCAAGGTCCTGGGGA
ACCCGAAGAGTGATGAGATGAATGTGAAGGTGCTGGACTTTGAGCATTTTCTGCCCATGCTGCAGACAGTGGCCAAGAAC
AAGGACCAGGGAACCTATGAGGATTATGTTGAAGGACTTCGAGTTTTTGACAAGGAAGGAAATGGCACCATCATGGAGGC
TGAAATCCGGCATGTTCTTGTCACACTGGGTGAGAAGATGACAGAGGAAGAAGTAGAGATGCTGGTGGCAGGGCACGAGG
ACAGCAATGGTTGTATCAACTACGAAGAGCTCGTCCGCATGGTGCTGAATGGCTGA

Alignment

ORF - retro_cjac_113 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.95 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHF
          MCDFT.DQT.EFKEAFQLFDRTGDGKILYSQCGDVMRALGQNP.NAEVLKVLGNPKSDEMNVKVLDFEHF
Retrocopy MCDFTKDQTTEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPNNAEVLKVLGNPKSDEMNVKVLDFEHF

Parental  LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN
          LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGT.M.AEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN
Retrocopy LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTIMEAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN

Parental  YEEFVRMV
          YEE.VRMV
Retrocopy YEELVRMV

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	24.52 RPM	122.52 RPM
SRP051959_heart	17.94 RPM	131.80 RPM
SRP051959_kidney	20.21 RPM	108.98 RPM
SRP051959_liver	13.80 RPM	77.09 RPM
SRP051959_lung	18.69 RPM	116.12 RPM
SRP051959_lymph_node	16.67 RPM	84.95 RPM
SRP051959_skeletal_muscle	5.00 RPM	41.12 RPM
SRP051959_spleen	20.48 RPM	114.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_113 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_113 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_113 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113 , retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,