RetrogeneDB ID: retro_cjac_3032

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:139360911..139361497(-)
• Located in intron of: ENSCJAG00000008922

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SOD2
• Ensembl ID: ENSCJAG00000011664
• Aliases: None
• Description: superoxide dismutase [Source:RefSeq peptide;Acc:NP_001254675]

Sequence

>retro_cjac_3032
TACAGTTGCCTAGGCTTGTCTGATGATTGTGGTGCCCTGGGGCCTAATAGTAATGTACAGATCATGCAGCTGAACCACAG
AAAATATCAGGTCGTTGGGTGAATAACTTGACTGCCCTCAAGGAGAAATAGGAGGTTCTGGTAAAAGGTGATGTTAGAAT
TCAGATAACTCTTCAGCCTGCACTTAAGTTTGGTGATGGAGACCGTATCACTCTTACCGTTTTATGGACAAACCTAAGCC
TCAGTGGTAGTGGAGGATTGAAAGGGGAGTTTCTGGGAGCCATGAAATGTTACTTTGGTTCCTTTGACTAACTTAAGAAG
AAGCTGACAGATGTATCCATTAGTATTCAAGGTTCCAGCTGTGGTTGGCTTGGTTTCATTAAGTAAAAAATCTCTTACAG
ATCATTGCTTGTCCTAATCAGGATCCATTGCAAGTATCGTCAGGTCTTATTCTACTCCAGGGGATTGATGTATGAGAGTT
TTCTTATTGTCTTCAGTATAAAAATGTCAGACTTCATTATCCAAAAGCTTTTTGGAGTGTAATCAACTGGGAAAATGTAA
CTGAAAGACCCACCGTTTGCAAAAAA

Alignment

ORF - retro_cjac_3032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.29 %
• Parental protein coverage: 88.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HSLPDLPYDYGALEPHINAQIMQLHHSKHHAA-YVNNLNDTEEKYKEALAKGDVTAQIALQPALKFNGGG
          .S...L..D.GAL.P..N.QIMQL.H.K......VNNL....EK..E.L.KGDV..QI.LQPALKF..G.
Retrocopy YSCLGLSDDCGALGPNSNVQIMQLNHRKYQVV<WVNNLTALKEK*-EVLVKGDVRIQITLQPALKFGDGD

Parental  HINHSIFWTNLSPDGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNK-ERGHLQIAA
          .I.....WTNLS..G.G..KGE.L.A.K..FGSFD..K.KLT..S...QGS..GWLGF.K.....LQI.A
Retrocopy RITLTVLWTNLSLSGSGGLKGEFLGAMKCYFGSFD*LKKKLTDVSISIQGSSCGWLGFIK<VKNLLQIIA

Parental  CPNQDPLQGTTGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK
          CPNQDPLQ...GLI.L.GIDV.E..Y.LQYKNVR..Y.KA.W.VINWENVTER...CKK
Retrocopy CPNQDPLQVSSGLILLQGIDV*EFSYCLQYKNVRLHYPKAFWSVINWENVTERPTVCKK

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	328.15 RPM
SRP051959_heart	0.04 RPM	167.39 RPM
SRP051959_kidney	0.00 RPM	401.30 RPM
SRP051959_liver	0.00 RPM	447.40 RPM
SRP051959_lung	0.00 RPM	209.62 RPM
SRP051959_lymph_node	0.00 RPM	103.76 RPM
SRP051959_skeletal_muscle	0.00 RPM	312.94 RPM
SRP051959_spleen	0.00 RPM	130.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3032 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3032 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3032 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1795
Equus caballus	retro_ecab_840

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015466	1 retrocopy	retro_amel_786,
Canis familiaris	ENSCAFG00000000671	1 retrocopy	retro_cfam_1795,
Choloepus hoffmanni	ENSCHOG00000003215	4 retrocopies	retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus	ENSCJAG00000011664	1 retrocopy	retro_cjac_3032 ,
Dasypus novemcinctus	ENSDNOG00000007907	1 retrocopy	retro_dnov_1653,
Equus caballus	ENSECAG00000011797	2 retrocopies	retro_ecab_70, retro_ecab_840,
Echinops telfairi	ENSETEG00000016400	1 retrocopy	retro_etel_731,
Felis catus	ENSFCAG00000002843	1 retrocopy	retro_fcat_1200,
Homo sapiens	ENSG00000112096	1 retrocopy	retro_hsap_430,
Gorilla gorilla	ENSGGOG00000008212	1 retrocopy	retro_ggor_419,
Myotis lucifugus	ENSMLUG00000012242	1 retrocopy	retro_mluc_528,
Monodelphis domestica	ENSMODG00000007521	1 retrocopy	retro_mdom_373,
Mustela putorius furo	ENSMPUG00000005045	1 retrocopy	retro_mputfur_1382,
Nomascus leucogenys	ENSNLEG00000011061	1 retrocopy	retro_nleu_1023,
Otolemur garnettii	ENSOGAG00000017100	1 retrocopy	retro_ogar_1123,
Pongo abelii	ENSPPYG00000017143	1 retrocopy	retro_pabe_292,
Pan troglodytes	ENSPTRG00000018757	1 retrocopy	retro_ptro_327,
Pteropus vampyrus	ENSPVAG00000005302	1 retrocopy	retro_pvam_288,
Rattus norvegicus	ENSRNOG00000019048	1 retrocopy	retro_rnor_2221,
Sarcophilus harrisii	ENSSHAG00000014795	1 retrocopy	retro_shar_210,
Ictidomys tridecemlineatus	ENSSTOG00000008738	1 retrocopy	retro_itri_1432,
Tupaia belangeri	ENSTBEG00000002100	1 retrocopy	retro_tbel_665,
Tarsius syrichta	ENSTSYG00000000457	1 retrocopy	retro_tsyr_183,
Tursiops truncatus	ENSTTRG00000014364	1 retrocopy	retro_ttru_265,