RetrogeneDB ID: retro_cjac_1812

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:72410811..72411867(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013380
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_1812
GGCATGTCCGTGTCCTCTGCCCGCTTCGTGTCCTCGTCCTCCTCCAGAGGGCTACGGTGGCATCCTGGCCGCAGCCGATG
TGCTGCTAGCGGGCAACGAGAAGCTCACCATGCAGAACCTCAACGACCGCCTGGCCACCTACCTGGACAAGGTGCGCGCC
CTGGAGGTGGCCAAAGGCGAGTTGGAAAAGATCCGCGACTGGTACCTGAAGCAGGGGACCCGGCCCTCCCACGACTACAG
CCACTACTACAAGACCATCCAGGACCTGCGGGACAAGATTCTTGGTGCCACCATTGAGAACTCCAGGATTGTCCTGCAGA
TCGACAGCGCCCATCTGGCTGCAGATGACTTCGAACCAAGTTTGAGACGGAGCAGGCTTTGCGCATGAGCGGGGAGGCCA
ACATCAAAGGCCTGCGCAGGATGCTGGATGAGCTGACCCTGGCCAGGAGCCATCTGGAGATGCAGATCGAAGAGCTGAAG
GAAGAGCTAGCCTATCTGAAGAAGAACCATGAGGAGGAAATCAGTGTGCTGAGGGGCCAAGTGGGAGGCAAGGTCCCTGT
GGAGGTGGATTCGGCTCCGGGTGCCAATCTCGTCAAGATCCTGAGTGACATGCGAAGTCAATGTGAGGTCCTGGTGGGGC
AGAACCGGAAGGATGCTGAATCCTGGTTCACCAGCCGGACTGAAGAACTGAACCGGGAGGTCGCTGGCCACACGGAGCAG
CTCCAAATGAACAAGACCGAGGTCGCTGACCTGTGGCGCACCCTCCAGGGTGTTGAGATCGAGCTGCAGTCACTGCTGAG
CACGAAAGCCGGCTTGGAAGGCACACTGGCAGAAATGGAGGTTCACTTTGGAGTCCAGCTGGCGGAGATCCAGGCGCGGA
TCAGCGGTATTGAAGCCTTGCTGGGTGATGTGCGGGCTGATAGTGAGAGGCAGAATCAAGAGTACCAGCGGGTCATGGAC
GTCAAGTCGCGGCTGGAGCAGGAGATCGCCACCTACCGCAGCCTGGTCGAGGATCAGGAAGATCGCTACAACAACCTGTC
TGCCTCCAAGGTCCTC

Alignment

ORF - retro_cjac_1812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.73 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVSVSSTRFVSSSSS-GGYGGGYGGILATSDGLLAGNEKLTMQNLNDRLASYLDKVRALEAANGELEVKI
          G.SVSS.RFVSSSSS..GYGG....ILA..D.LLAGNEKLTMQNLNDRLA.YLDKVRALE.A.GELE.KI
Retrocopy GMSVSSARFVSSSSS>EGYGG----ILAAADVLLAGNEKLTMQNLNDRLATYLDKVRALEVAKGELE-KI

Parental  RDWYQKQGPGPSRDYSHYYKTIQDLRDQILGATIENSRIVLQIDNARLAADDF-RTKFETEQALRMSVEA
          RDWY.KQG..PS.DYSHYYKTIQDLRD.ILGATIENSRIVLQID.A.LAADDF.RTKFETEQALRMS.EA
Retrocopy RDWYLKQGTRPSHDYSHYYKTIQDLRDKILGATIENSRIVLQIDSAHLAADDF<RTKFETEQALRMSGEA

Parental  DINGLRRVLDELTLARTDLEMQIEGLKEELAYLKKNHEEELSVLRGQVGGQVSVEVDSAPGTDLAKILSD
          .I.GLRR.LDELTLAR..LEMQIE.LKEELAYLKKNHEEE.SVLRGQVGG.V.VEVDSAPG..L.KILSD
Retrocopy NIKGLRRMLDELTLARSHLEMQIEELKEELAYLKKNHEEEISVLRGQVGGKVPVEVDSAPGANLVKILSD

Parental  MRSQYEVMAEQNRKDAEAWFTSRSEELNREVAVHREQLQMSNTEVSDLRRTLQGLEIELQSQLSMKAGLE
          MRSQ.EV...QNRKDAE.WFTSR.EELNREVA.H.EQLQM..TEV.DL.RTLQG.EIELQS.LS.KAGLE
Retrocopy MRSQCEVLVGQNRKDAESWFTSRTEELNREVAGHTEQLQMNKTEVADLWRTLQGVEIELQSLLSTKAGLE

Parental  STLAETEARFGAQLAEIQARISGIEAQLGDVRADSERQNQEYHRLLDVKSRLEQEIATYRSLLEGQEDRY
          .TLAE.E..FG.QLAEIQARISGIEA.LGDVRADSERQNQEY.R..DVKSRLEQEIATYRSL.E.QEDRY
Retrocopy GTLAEMEVHFGVQLAEIQARISGIEALLGDVRADSERQNQEYQRVMDVKSRLEQEIATYRSLVEDQEDRY

Parental  NNLSASKVL
          NNLSASKVL
Retrocopy NNLSASKVL

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	0.00 RPM	290.23 RPM
SRP051959_heart	0.04 RPM	4.95 RPM
SRP051959_kidney	0.02 RPM	2.37 RPM
SRP051959_liver	0.00 RPM	1.75 RPM
SRP051959_lung	0.03 RPM	44.90 RPM
SRP051959_lymph_node	0.00 RPM	0.32 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.09 RPM
SRP051959_spleen	0.00 RPM	1.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1812 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1812 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1812 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,