RetrogeneDB ID: retro_cjac_3289

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:35859897..35860537(-)
• Located in intron of: ENSCJAG00000008072

Retrocopy information

• Ensembl ID: ENSCJAG00000008124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001215
• Aliases: None
• Description: None

Sequence

>retro_cjac_3289
GTACACCGAAGTATAGAGGGCTGCTGTATTTGCAGAGCTAAGTCCTCCAGTTCTCGATTCACTGACAGTAAACGCTATGA
AAAGGACTTCCAGAGCTGTTTTGGATTGCATGAGACTCGTTCAGGAGACATCTGCAATGCCTGTGTCCTGCTTGTGAAAA
GATGGAAGAAGTTGCCAGCAGGATCAAAAAAAAAACTGGAATCATGTGGTAGATGCAAGGGCTGGACCCAGTCTAAAGAC
TACATTGAAACCAAAGAAAGTGAAAACTTTATCTGGGAACAGGATAAAAAGCAACCATATCAGTAAACTGCAGAAGGAAT
TTAAACGTCATAATTCTGATGCTCACAGTACCACCTCAAGTGCCTCCCCAGCTCAATCTCCTTGTTACAGTAACCAGTCA
GATGACGGCTCAGACACAGAGATGGCTTCTGGTTCTAACAGAACACCAGTTTTTTCCTTTTTAGATCTCACATACTGGAA
AAGACAGAAGATTTGTTGTGGGATCATCTATAAAGGCCGTTGTGGCGAAGTCCTCATTGATACACATCTCTTCAAGCCTT
GCTGTAGCAATAAGAAAGCAGCTGCTGAGAAGCCAGAGGAGCAAGGGCCAGAGCCTCTGCCCATGTCCACTCAGGAGTGG

Alignment

ORF - retro_cjac_3289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.2 %
• Parental protein coverage: 96.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGSKK-NWNHV
          ..RSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGSKK.NWNHV
Retrocopy VHRSIEGCCICRAKSSSSRFTDSKRYEKDFQSCFGLHETRSGDICNACVLLVKRWKKLPAGSKK>NWNHV

Parental  VDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQKEFKRHNSDAHSTTSSASPAQSPCYSNQSDDGSDT
          VDARAGPSLKTTLKPKKVKTLSGNRIKSN.ISKLQKEFKRHNSDAHSTTSSASPAQSPCYSNQSDDGSDT
Retrocopy VDARAGPSLKTTLKPKKVKTLSGNRIKSNHISKLQKEFKRHNSDAHSTTSSASPAQSPCYSNQSDDGSDT

Parental  EMASGSNRTPVFSFLDLTYWKRQKICCGIIYKGRFGEVLIDTHLFKPCCSNKKAAAEKPEEQGPEPLPIS
          EMASGSNRTPVFSFLDLTYWKRQKICCGIIYKGR.GEVLIDTHLFKPCCSNKKAAAEKPEEQGPEPLP.S
Retrocopy EMASGSNRTPVFSFLDLTYWKRQKICCGIIYKGRCGEVLIDTHLFKPCCSNKKAAAEKPEEQGPEPLPMS

Parental  TQEW
          TQEW
Retrocopy TQEW

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	0.22 RPM	17.64 RPM
SRP051959_heart	0.88 RPM	12.86 RPM
SRP051959_kidney	0.75 RPM	26.31 RPM
SRP051959_liver	0.30 RPM	6.48 RPM
SRP051959_lung	0.23 RPM	22.45 RPM
SRP051959_lymph_node	0.62 RPM	33.31 RPM
SRP051959_skeletal_muscle	0.17 RPM	3.10 RPM
SRP051959_spleen	0.57 RPM	23.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3289 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001161	1 retrocopy	retro_btau_1020,
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Choloepus hoffmanni	ENSCHOG00000007193	17 retrocopies	retro_chof_109, retro_chof_1108, retro_chof_1136, retro_chof_1255, retro_chof_1614, retro_chof_1689, retro_chof_1770, retro_chof_1971, retro_chof_2126, retro_chof_2493, retro_chof_2576, retro_chof_2587, retro_chof_453, retro_chof_511, retro_chof_856, retro_chof_979, retro_chof_998,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289 ,
Dasypus novemcinctus	ENSDNOG00000016873	2 retrocopies	retro_dnov_1674, retro_dnov_2668,
Equus caballus	ENSECAG00000009655	2 retrocopies	retro_ecab_287, retro_ecab_385,
Erinaceus europaeus	ENSEEUG00000012617	2 retrocopies	retro_eeur_350, retro_eeur_372,
Echinops telfairi	ENSETEG00000002888	2 retrocopies	retro_etel_1087, retro_etel_427,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Homo sapiens	ENSG00000139146	3 retrocopies	retro_hsap_1928, retro_hsap_1945, retro_hsap_4029,
Gorilla gorilla	ENSGGOG00000015484	3 retrocopies	retro_ggor_1405, retro_ggor_1415, retro_ggor_2704,
Microcebus murinus	ENSMICG00000003460	2 retrocopies	retro_mmur_1176, retro_mmur_409,
Myotis lucifugus	ENSMLUG00000009827	3 retrocopies	retro_mluc_1663, retro_mluc_1672, retro_mluc_765,
Macaca mulatta	ENSMMUG00000009155	2 retrocopies	retro_mmul_1074, retro_mmul_2324,
Mus musculus	ENSMUSG00000039985	4 retrocopies	retro_mmus_1234, retro_mmus_1471, retro_mmus_1557, retro_mmus_3331,
Nomascus leucogenys	ENSNLEG00000016487	1 retrocopy	retro_nleu_1213,
Oryctolagus cuniculus	ENSOCUG00000008618	1 retrocopy	retro_ocun_1176,
Otolemur garnettii	ENSOGAG00000008927	4 retrocopies	retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Pongo abelii	ENSPPYG00000004396	2 retrocopies	retro_pabe_1592, retro_pabe_3309,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,
Tursiops truncatus	ENSTTRG00000008465	3 retrocopies	retro_ttru_1162, retro_ttru_1498, retro_ttru_984,