RetrogeneDB ID: retro_cjac_3108

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:7883774..7884505(-)
• Located in intron of: ENSCJAG00000007656

Retrocopy information

• Ensembl ID: ENSCJAG00000007667
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRT19
• Ensembl ID: ENSCJAG00000029756
• Aliases: None
• Description: None

Sequence

>retro_cjac_3108
ACTTCTTACAGCTATCGCCAGTCGTCTGCCACGTCCTCCTTCGGGGCTTCTGGGCGGCGGCTCCGTGCATTTTTGGCTGG
AGATCGCCTTTCGCGCTCCCAGTATGCACGGGAGCTTCAGAGGCCGCGGGGCATGTCCATGTCCTCCGCCGGCTTCGTGT
CTTTGTCTTTCTTAGGGGGCTACAGCGGCGGCTATGGCGGCGTCCTAGCAGCATCCAATGAGCTGCTGGCCGGCAAGGAG
AAGCTCACCATGCAGAACCTCAACAACCACCTTGGCCTCCTACCTGGAAAAGGTGCGCGCCCTGGAGGAAGCCAATGGCA
AGCTGGAAGTGAAGATCCGCGACTGGTACCAGAAGCAGGGGCCCCGGGCCCTCCCGCTACTATAGCCATTACTACAAGAC
CATCCAGGATCTGAGGGACAAGATTCTTGGTGCCACCATTGAGAACTCCAGGACTGTCCTGCAGATCGACAACACCCATC
TGGCTGCAGATGACTTCCGAACCAAGTTTGAGACAGAGCAGGCTTTGCACATGAACGTGGAGGTCGACATCAATGGCCAG
CGCAGGGTGCTGGATGAGCTGACCCTGGCCAGGACCGATCTCGAGATGCAGATAGAAGGACTGAAGGAAGAGCTGGCCTA
CCTGAAGAACAGCCATGAGGAGGAAATCAGCGCACTGAGGGGCCAAGTGGGAGGCCAGGTCAGTGTGGAGGTGGATTCGG
CTCCAAGCACC

Alignment

ORF - retro_cjac_3108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TSYSYRQSS-TSSFGG-LGGASVRFGPGVAFRA-PSIHGGSGG-RGVSVSSTRFVSSSSSGGYGGGYGGI
          TSYSYRQSS.TSSFG..LGG.SV.F....AFRA.P...G.S...RG.S.SS..FVS.S..GGY.GGYGG.
Retrocopy TSYSYRQSSATSSFGA>LGGGSVHFWLEIAFRA>PVCTGASEA>RGMSMSSAGFVSLSFLGGYSGGYGGV

Parental  LATSDGLLAGNEKLTMQNLNDRL-ASYLDKVRALEAANGELEVKIRDWYQKQGP-GPSRDYSHYYKTIQD
          LA.S..LLAG.EKLTMQNLN..L.ASYL.KVRALE.ANG.LEVKIRDWYQKQGP.GPSR.YSHYYKTIQD
Retrocopy LAASNELLAGKEKLTMQNLNNHL>ASYLEKVRALEEANGKLEVKIRDWYQKQGP>GPSRYYSHYYKTIQD

Parental  LRDQILGATIENSRIVLQIDNARLAADDFRTKFETEQALRMSVEADINGLRRVLDELTLARTDLEMQIEG
          LRD.ILGATIENSR.VLQIDN..LAADDFRTKFETEQAL.M.VE.DING.RRVLDELTLARTDLEMQIEG
Retrocopy LRDKILGATIENSRTVLQIDNTHLAADDFRTKFETEQALHMNVEVDINGQRRVLDELTLARTDLEMQIEG

Parental  LKEELAYLKKNHEEELSVLRGQVGGQVSVEVDSAPGT
          LKEELAYLK..HEEE.S.LRGQVGGQVSVEVDSAP.T
Retrocopy LKEELAYLKNSHEEEISALRGQVGGQVSVEVDSAPST

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	0.04 RPM	290.23 RPM
SRP051959_heart	0.02 RPM	4.95 RPM
SRP051959_kidney	0.20 RPM	2.37 RPM
SRP051959_liver	0.09 RPM	1.75 RPM
SRP051959_lung	0.05 RPM	44.90 RPM
SRP051959_lymph_node	0.00 RPM	0.32 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.09 RPM
SRP051959_spleen	0.02 RPM	1.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3108 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3108 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108 , retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,