RetrogeneDB ID: retro_cjac_3085

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:77680801..77681323(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSCJAG00000001066
• Aliases: None
• Description: None

Sequence

>retro_cjac_3085
ACAAGGGCACAAAGACTCCTCATCCTAAACAAAGTATTAAGGAACATGGTTTATGTGCAGCAAAGCAGGGAGTCTAGCCT
GAAATACCAGACTGGCTGCATGCAAGCCTTTCCAAACAAGCAGGGTTATGTATTAAGCTCTATCAAAGGCCAAGTGGCAG
TTGAATACTTGGACCCAAACCCTGAGGTACAGAAGAAGAAATATGCTGTCAAATGTCTCAGACTAAAAGAACAAAATATT
GAGTAGGTTTACCCATTCAATGCCATTTCTTTCCACAATATCCACAATACATTTGCCACAGGTGGTTCTGATGCCTTTGT
AAATATTTGGGATCCATTTAACAAAAAGCAACGGTGCCAGTTCCATCGTTACCCCATGAGCATCGCATCACTTCCCTTCA
GTAATGATGGGGCTACGCTGACAAGAGCATCATCATGTATGTATGAAATGGATGACATGGAATATCCTGAAAATGGCATC
TTCATTCGCCAAGTGACAGATGCAGAAATGTAACCCAAGTCC

Alignment

ORF - retro_cjac_3085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.16 %
• Parental protein coverage: 52.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAGRRVLVWD--LRNMGYVQQRRESSLKYQTRCIRAFPNKQGYVLSSIEGRVAVEYLDPSPEIQKKKYAF
          T...R.L.....LRNM.YVQQ.RESSLKYQT.C..AFPNKQGYVLSSI.G.VAVEYLDP.PE.QKKKYA.
Retrocopy TRAQRLLILNKVLRNMVYVQQSRESSLKYQTGCMQAFPNKQGYVLSSIKGQVAVEYLDPNPEVQKKKYAV

Parental  KCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVNIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTL
          KC.RLKE.NIE..YP.NAISFHNIHNTFATGGSD.FVNIWDPFNKK..CQFHRYP.SIASL.FSNDG.TL
Retrocopy KCLRLKEQNIE*VYPFNAISFHNIHNTFATGGSDAFVNIWDPFNKKQRCQFHRYPMSIASLPFSNDGATL

Parental  AIASSYMYEMDDTEHPEDGIFIRQVTDAETKPKS
          ..ASS.MYEMDD.E.PE.GIFIRQVTDAE..PKS
Retrocopy TRASSCMYEMDDMEYPENGIFIRQVTDAEM*PKS

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	34.63 RPM
SRP051959_heart	0.00 RPM	20.45 RPM
SRP051959_kidney	0.00 RPM	23.69 RPM
SRP051959_liver	0.39 RPM	25.60 RPM
SRP051959_lung	0.00 RPM	27.36 RPM
SRP051959_lymph_node	0.00 RPM	44.70 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.93 RPM
SRP051959_spleen	0.00 RPM	34.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3085 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3085 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012700	1 retrocopy	retro_cfam_399,
Callithrix jacchus	ENSCJAG00000001066	1 retrocopy	retro_cjac_3085 ,
Cavia porcellus	ENSCPOG00000011957	1 retrocopy	retro_cpor_997,
Homo sapiens	ENSG00000154473	1 retrocopy	retro_hsap_3887,
Gorilla gorilla	ENSGGOG00000023971	1 retrocopy	retro_ggor_2614,
Myotis lucifugus	ENSMLUG00000017732	1 retrocopy	retro_mluc_627,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729,
Nomascus leucogenys	ENSNLEG00000027075	1 retrocopy	retro_nleu_1887,
Procavia capensis	ENSPCAG00000007736	1 retrocopy	retro_pcap_412,
Pongo abelii	ENSPPYG00000002731	1 retrocopy	retro_pabe_3168,
Ictidomys tridecemlineatus	ENSSTOG00000021785	1 retrocopy	retro_itri_1095,
Tarsius syrichta	ENSTSYG00000013444	2 retrocopies	retro_tsyr_1652, retro_tsyr_732,
Tursiops truncatus	ENSTTRG00000016194	1 retrocopy	retro_ttru_1136,