RetrogeneDB ID: retro_cjac_488

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:183959054..183960032(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007254
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004644
• Aliases: None
• Description: None

Sequence

>retro_cjac_488
ATGGACCCCCCCAAAGTGAACGAGCTTCGGGCCTTTGTGAAGATGTGTAAGCAGGATCCAAGCGTTCTGCACACAGAGGA
AATGCGCTTCCTGAGGGAGTGGGTGGAGAGTACGGGTGGGAAAATACCACCTGCTACTCAGAAAGCTAAATCAGAAGAAA
ATGCCAAGGAAGAAAACCTGATAGTAAGAAGGCAGAGGAAGACTTAAAGGCAGACGAACCATCAAGTGAGGAAAGTGATC
TGGAAACTGATAATGAAGGTGTGATTGAACCAGACACTGACACCCCTCAAGAAATGGGAGATGAAACTGCAGAGATAACA
GAGGGATGATGGATCAGGCAAATGATAAGAAAGTGGCTGCTATTGTAGCCCTAAATGATGGTGAATTGCAGAAAGCCATT
GACTTATTCACAGATGCCATCAAGCTGAATCCTCGCTTGGCCATTTTGTATGCCAAGAGGGCCAGTGTCTTCGTCACATT
ACAGAAGCCAAATGCTGCCATCCGAGACTGTGACAGAGCCATTTAAAGAAATCCTGATTCAGCTCAGCCTTACAAGTGGC
GAGGGAAAGCACACAGACTTCTAGGCCACTGGGAAGAAGCAGCCCATGATCTTGCCCTTGCCTGTAAATGGGATTATGCT
GAAGATGCGAGTGCAATGCTGAAAGAAGTTCAACCTAGGGCACAGAAAACTGCGAACATCGGAGAAAGGATGAGCGAAAA
CGTGAGGAGCGAGAGATCAAAGAAAGAATAGAAAGAGTTAAGAAGGCTCGAGAAGAGCATGAGAGAGCCCAGAGGGAGGA
AGAAGCCAGACGACAGTCAGGAGCTCAGTATGGCTCTTTTCCAGGTGGCTTTCCTGGGGGAATGCCTGGTGGTTTTCCCG
GAGGAATGCCTGGAATGGGAGGGGGCATGCCTGGAATGGCCGGAATGCCTGGACTCAGTGAGATTCTTAGTGATCCAGAG
GTTCTCGCAGCCATGAAG

Alignment

ORF - retro_cjac_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 88.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDPRKVNELRAFVKMCKQDPSVLHTEEMRFLREWVESMGGKIPPATQKAKSEENTKEE-KPDSKKVEEDL
          MDP.KVNELRAFVKMCKQDPSVLHTEEMRFLREWVES.GGKIPPATQKAKSEEN.KEE.KPDSKK.EEDL
Retrocopy MDPPKVNELRAFVKMCKQDPSVLHTEEMRFLREWVESTGGKIPPATQKAKSEENAKEE<KPDSKKAEEDL

Parental  KADEPSSEESDLEIDNEGVIEPDTDTPQEMGDENAEITEE-MMDQANDKKVAAIEALNDGELQKAIDLFT
          KADEPSSEESDLE.DNEGVIEPDTDTPQEMGDE.AEITE..MMDQANDKKVAAI.ALNDGELQKAIDLFT
Retrocopy KADEPSSEESDLETDNEGVIEPDTDTPQEMGDETAEITEG<MMDQANDKKVAAIVALNDGELQKAIDLFT

Parental  DAIKLNPRLAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEAAAHDLALA
          DAIKLNPRLAILYAKRASVFV.LQKPNAAIRDCDRAI..NPDSAQPYKWRGKAHRLLGHWE.AAHDLALA
Retrocopy DAIKLNPRLAILYAKRASVFVTLQKPNAAIRDCDRAI*RNPDSAQPYKWRGKAHRLLGHWEEAAHDLALA

Parental  CKLDYDEDASAMLKEVQPRAQKIA-EHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQSGAQ
          CK.DY.EDASAMLKEVQPRAQK.A.EHRRK.ERKREEREIKERIERVKKAREEHERAQREEEARRQSGAQ
Retrocopy CKWDYAEDASAMLKEVQPRAQKTA<EHRRKDERKREEREIKERIERVKKAREEHERAQREEEARRQSGAQ

Parental  YGSFPGGFPGGMPGGFPGGMPGMGGGMPGMAGMPGLNEILSDPEVLAAMQ
          YGSFP.................MGGGMPGMAGMPGL.EILSDPEVLAAM.
Retrocopy YGSFPXXXXXXXXXXXXXXXXXMGGGMPGMAGMPGLSEILSDPEVLAAMK

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	0.02 RPM	51.81 RPM
SRP051959_heart	0.02 RPM	52.32 RPM
SRP051959_kidney	0.09 RPM	129.52 RPM
SRP051959_liver	0.04 RPM	118.48 RPM
SRP051959_lung	0.20 RPM	59.25 RPM
SRP051959_lymph_node	0.09 RPM	61.85 RPM
SRP051959_skeletal_muscle	0.07 RPM	80.10 RPM
SRP051959_spleen	0.02 RPM	61.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_488 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005227	1 retrocopy	retro_acar_2,
Ailuropoda melanoleuca	ENSAMEG00000013880	1 retrocopy	retro_amel_135,
Bos taurus	ENSBTAG00000006202	4 retrocopies	retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris	ENSCAFG00000001139	14 retrocopies	retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Choloepus hoffmanni	ENSCHOG00000012676	1 retrocopy	retro_chof_2222,
Callithrix jacchus	ENSCJAG00000004644	11 retrocopies	retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488 , retro_cjac_640, retro_cjac_685,
Cavia porcellus	ENSCPOG00000002290	4 retrocopies	retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus	ENSFCAG00000011847	2 retrocopies	retro_fcat_920, retro_fcat_987,
Homo sapiens	ENSG00000100380	16 retrocopies	retro_hsap_1055, retro_hsap_1203, retro_hsap_178, retro_hsap_201, retro_hsap_2078, retro_hsap_2189, retro_hsap_2853, retro_hsap_3206, retro_hsap_3907, retro_hsap_4009, retro_hsap_4876, retro_hsap_500, retro_hsap_619, retro_hsap_756, retro_hsap_812, retro_hsap_986,
Gorilla gorilla	ENSGGOG00000026747	16 retrocopies	retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Microcebus murinus	ENSMICG00000008875	2 retrocopies	retro_mmur_481, retro_mmur_954,
Myotis lucifugus	ENSMLUG00000007764	2 retrocopies	retro_mluc_1088, retro_mluc_2021,
Macaca mulatta	ENSMMUG00000019118	3 retrocopies	retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica	ENSMODG00000013042	2 retrocopies	retro_mdom_1087, retro_mdom_31,
Mustela putorius furo	ENSMPUG00000016432	15 retrocopies	retro_mputfur_1640, retro_mputfur_211, retro_mputfur_212, retro_mputfur_233, retro_mputfur_272, retro_mputfur_282, retro_mputfur_289, retro_mputfur_343, retro_mputfur_373, retro_mputfur_379, retro_mputfur_402, retro_mputfur_450, retro_mputfur_506, retro_mputfur_605, retro_mputfur_778,
Mus musculus	ENSMUSG00000022403	2 retrocopies	retro_mmus_2997, retro_mmus_651,
Nomascus leucogenys	ENSNLEG00000015378	17 retrocopies	retro_nleu_1142, retro_nleu_1155, retro_nleu_1606, retro_nleu_1852, retro_nleu_2075, retro_nleu_2088, retro_nleu_2376, retro_nleu_2404, retro_nleu_247, retro_nleu_2555, retro_nleu_2765, retro_nleu_3121, retro_nleu_3122, retro_nleu_319, retro_nleu_447, retro_nleu_552, retro_nleu_988,
Otolemur garnettii	ENSOGAG00000016932	1 retrocopy	retro_ogar_224,
Pongo abelii	ENSPPYG00000011858	14 retrocopies	retro_pabe_1004, retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pelodiscus sinensis	ENSPSIG00000004553	1 retrocopy	retro_psin_42,
Pteropus vampyrus	ENSPVAG00000011908	2 retrocopies	retro_pvam_1104, retro_pvam_393,
Rattus norvegicus	ENSRNOG00000019070	8 retrocopies	retro_rnor_1360, retro_rnor_1725, retro_rnor_1798, retro_rnor_1976, retro_rnor_2204, retro_rnor_2372, retro_rnor_2481, retro_rnor_2543,
Sarcophilus harrisii	ENSSHAG00000000319	2 retrocopies	retro_shar_70, retro_shar_767,
Sus scrofa	ENSSSCG00000000071	1 retrocopy	retro_sscr_428,
Ictidomys tridecemlineatus	ENSSTOG00000003165	1 retrocopy	retro_itri_88,
Tursiops truncatus	ENSTTRG00000011510	5 retrocopies	retro_ttru_1245, retro_ttru_1425, retro_ttru_1615, retro_ttru_385, retro_ttru_670,