RetrogeneDB ID: retro_cjac_1665

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:7964784..7965367(-)
• Located in intron of: ENSCJAG00000009801

Retrocopy information

• Ensembl ID: ENSCJAG00000009925
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DENR
• Ensembl ID: ENSCJAG00000020488
• Aliases: None
• Description: density-regulated protein [Source:HGNC Symbol;Acc:2769]

Sequence

>retro_cjac_1665
GACATTTCTGAATCCAGCGGGGCTGATTGCAAAGGAGACCCAAGGAACAGTGCCAAGTTAGATGCCGATTACCCACTTCA
AGTCCTTTATTGTGGAGTCTGTTCATTACCAACAGAGTACTGTGAATATATGCCTAATGTTGCTAAATGTAGACAATGGT
TAGAGAAGAATTTTCCAAATGAATTTGCAAAACTTACTGTAGAAAATTCACCCAAACAAGAAACTGGAATTAATGAGGGT
CAAGGAACAGCAGGGGAAGAAGAGAAGAAAAAACAGAAGAGAGGTAGAAGGGGTCAAATAAAGACAAAAACAGAAGACTG
TACCACAAAAGGTTACTGTAGCCAAAATTCCCAGAGCAAAAAAGAAATATGTGACAAGAGTGTGTGGCCTTGCAACTTTT
GGAATTGATCTTAAAGAAGCACAAAGATTTTTTGCTCAGAAATTCTCCTGTGGTGCCTCAGTAACAGGGGAGGATGAAAT
TATCATTCAGGGAGACTTTACAGATGACATAATTGATGTCATTCAGGAAAAGTGGCCAGAGGTAGATGGTGACAGCATTG
AAGATCTTGGAGAAGTGAAGAAG

Alignment

ORF - retro_cjac_1665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 98.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DISESSGADCKGDPRNSAKLDADYPLRVLYCGVCSLPTEYCEYMPDVAKCRQWLEKNFPNEFAKLTVARK
          DISESSGADCKGDPRNSAKLDADYPL.VLYCGVCSLPTEYCEYMP.VAKCRQWLEKNFPNEFAKLTV...
Retrocopy DISESSGADCKGDPRNSAKLDADYPLQVLYCGVCSLPTEYCEYMPNVAKCRQWLEKNFPNEFAKLTV--E

Parental  YTPKQETGISEGQGTAGGSQRKKKLNKGGRGQIK-QKKKTVPQKVTIAKIPRAKKKYVTRVCGLATFEIE
          ..PKQETGI.EGQGTA.G...KKK...G.RGQIK.QK.KTVPQKVT.AKIPRAKKKYVTRVCGLATF...
Retrocopy NSPKQETGINEGQGTA-GEEEKKKQKRGRRGQIK>QKQKTVPQKVTVAKIPRAKKKYVTRVCGLATF--G

Parental  IDLKEAQRFFAQKFSCGASVTGEDEIIIQGDFTDDIIDVIQEKWPEVDDDSIEDLGEVKK
          IDLKEAQRFFAQKFSCGASVTGEDEIIIQGDFTDDIIDVIQEKWPEVD.DSIEDLGEVKK
Retrocopy IDLKEAQRFFAQKFSCGASVTGEDEIIIQGDFTDDIIDVIQEKWPEVDGDSIEDLGEVKK

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	1.15 RPM	4.28 RPM
SRP051959_heart	0.61 RPM	3.51 RPM
SRP051959_kidney	1.40 RPM	4.93 RPM
SRP051959_liver	1.45 RPM	5.94 RPM
SRP051959_lung	0.91 RPM	3.24 RPM
SRP051959_lymph_node	1.44 RPM	5.23 RPM
SRP051959_skeletal_muscle	1.18 RPM	3.78 RPM
SRP051959_spleen	1.39 RPM	5.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1665 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016012	1 retrocopy	retro_acar_71,
Bos taurus	ENSBTAG00000032433	1 retrocopy	retro_btau_110,
Callithrix jacchus	ENSCJAG00000020488	4 retrocopies	retro_cjac_1665 , retro_cjac_2303, retro_cjac_2377, retro_cjac_2627,
Echinops telfairi	ENSETEG00000013029	1 retrocopy	retro_etel_1127,
Homo sapiens	ENSG00000139726	4 retrocopies	retro_hsap_1028, retro_hsap_1854, retro_hsap_2471, retro_hsap_4313,
Gorilla gorilla	ENSGGOG00000005562	3 retrocopies	retro_ggor_2156, retro_ggor_2883, retro_ggor_813,
Myotis lucifugus	ENSMLUG00000002088	1 retrocopy	retro_mluc_2450,
Nomascus leucogenys	ENSNLEG00000002186	3 retrocopies	retro_nleu_1465, retro_nleu_2136, retro_nleu_906,
Oryctolagus cuniculus	ENSOCUG00000008150	2 retrocopies	retro_ocun_1325, retro_ocun_1524,
Ochotona princeps	ENSOPRG00000015974	5 retrocopies	retro_opri_1000, retro_opri_1139, retro_opri_1147, retro_opri_133, retro_opri_183,
Pongo abelii	ENSPPYG00000005073	3 retrocopies	retro_pabe_1821, retro_pabe_3509, retro_pabe_861,
Pan troglodytes	ENSPTRG00000005584	4 retrocopies	retro_ptro_1236, retro_ptro_2921, retro_ptro_2955, retro_ptro_703,
Sorex araneus	ENSSARG00000004446	4 retrocopies	retro_sara_118, retro_sara_125, retro_sara_523, retro_sara_722,
Sus scrofa	ENSSSCG00000009788	1 retrocopy	retro_sscr_1145,
Tursiops truncatus	ENSTTRG00000015856	1 retrocopy	retro_ttru_745,
Vicugna pacos	ENSVPAG00000011472	1 retrocopy	retro_vpac_139,