RetrogeneDB ID: retro_cjac_2848

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:124255550..124256147(-)
• Located in intron of: ENSCJAG00000002759

Retrocopy information

• Ensembl ID: ENSCJAG00000002825
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2848
AAGAAGGATGTTCTTTCTGGGGAGGAAGCAGCAGGGCCCTACCTCTCCAAACCTGCTGCCAACCAGCAGCAGCAGGGGTC
TCTCCAACCAAAATCAAAGCTGAGCCAGCTATTCCCCTAAACCCCTGAGAAAGCCCAGGAGCCCTTAATCAATCTCTCCA
AAGTGGTGATCAGGTTTAACAAGGACCAGTTGGAGGAGCTCAAGGAGGCCTTCAAGCTGTTTGGCAGAGTGCAGGATGGC
AAGATCCTGTACAGCCAGTTTGGGGACATGATGGGGGCCCTGGGCCAGAACCCCACCAATGCCAAGGTGCTCAGAGTCCT
AGGGAACCCCAAGAGTGATGAGCTGAAGTCCCAGCATGTGGACTTAAAGACTTTCCTGCCCATGCTCCAAGCAGCAGCCA
AGAACCGGAACCAGGGCACATATGAGGACTACTTGGAAGGGCTTCACGTGTTTGACAACAGCAAAGTTAGGAGAGCTGAG
CTCAGACAAGCCCTTACCACCCTGGGAGAGAAGATAGCTGAAGAGGAGATGGAGACTGTTCTGGCAGGACATGAGGTCAG
CAACGGCTGCATCAACTACGAGGCCTTCCTAAAACAT

Alignment

ORF - retro_cjac_2848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKDV-PVKKPAGPSISKPAT-KPAAAGAPPAKPKAEPAVPQ-APQKTQEPPVDLSKVVIEFNKDQLEEFK
          KKDV......AGP..SKPA...PAAAG..P.K.KAEPA.P...P.K.QEP...LSKVVI.FNKDQLEE.K
Retrocopy KKDVLSGEEAAGPYLSKPAA<QPAAAGVSPTKIKAEPAIPL>TPEKAQEPLINLSKVVIRFNKDQLEELK

Parental  EAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKILGNPKSDELKSRRVDFETFLPMLQAVAKNRDQ
          EAF.LF.RV.DGKILYSQ.GD.M.ALGQNPTNA.VL..LGNPKSDELKS..VD..TFLPMLQA.AKNR.Q
Retrocopy EAFKLFGRVQDGKILYSQFGDMMGALGQNPTNAKVLRVLGNPKSDELKSQHVDLKTFLPMLQAAAKNRNQ

Parental  GTYEDYLEGLRVFDKEGNGKVMGAELRHVLTTLGEKMTEEEVEMLVAGHEDSNGCINYEAFVRH
          GTYEDYLEGL.VFD...N.KV..AELR..LTTLGEK..EEE.E...AGHE.SNGCINYEAF..H
Retrocopy GTYEDYLEGLHVFD---NSKVRRAELRQALTTLGEKIAEEEMETVLAGHEVSNGCINYEAFLKH

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	0.18 RPM	122.52 RPM
SRP051959_heart	0.07 RPM	131.80 RPM
SRP051959_kidney	0.09 RPM	108.98 RPM
SRP051959_liver	0.06 RPM	77.09 RPM
SRP051959_lung	0.13 RPM	116.12 RPM
SRP051959_lymph_node	0.18 RPM	84.95 RPM
SRP051959_skeletal_muscle	0.09 RPM	41.12 RPM
SRP051959_spleen	0.06 RPM	114.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2848 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2848 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2383
Pan troglodytes	retro_ptro_1741
Gorilla gorilla	retro_ggor_1808
Pongo abelii	retro_pabe_2150
Macaca mulatta	retro_mmul_962

---

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,