RetrogeneDB ID: retro_cjac_3938

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286345.1:13914..15222(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX10
• Ensembl ID: ENSCJAG00000004522
• Aliases: None
• Description: Protoheme IX farnesyltransferase, mitochondrial [Source:UniProtKB/TrEMBL;Acc:F6VLK0]

Sequence

>retro_cjac_3938
ACATTCTCCTCACGCCTCCTGACAGGTTGCGTAGGAGGATGTGTCTGGTATCTTGAAAGAATAATAATACAGGTATCCCC
TCACAAGTTCTTGCATCTTGTCAGGAATGTCAATGAGCAGTGGATTACATTTCAGCACTTTAGCTTCCTCAGACGCATGT
ATGTCACACGGCTGAACAGAAGTCACAACCAGCAAGTAAAACCCAAGCCAGAACACGTAGCATCTACTTTCCTTGAAAAA
ACATCTTCAGGTCAAGCCAAAGCAGAAATATATGAGACGAGACCTCTTTTACCACCCAGCCTTTCTTTGTCCAGAAAACC
AAATGAAAAGGAATTGATAGAACTAGAGCTGGCCTCAGAAATTGAAGACCCAATAGATGTAGGGAAAGAGACAAAAGACG
AAAAGCAGTGAAAAGAGATGAAGATGCAAGTGAGTGATTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAAGTCACA
GAGCTGGTAGTAAGTACCACTTCAGCTGGATTTGTATTGGCTTTAGGCCCTTTTGACTTGCCCTGTTTCCTGCTTACTTC
TATTGGGACAGGCCTCACATCCTGCGCTGCCAACTCCATCAGTCGGTTTTTTGAGGTACCATTTGACTCAAACATGAATA
GGACAAAGAACAGACCTCCGGTTCGTGGAGAGATCAGCCCATTGTTAGCTGTGTCTTTTGCCACTTGATGTGCTGTTCCC
GGGGTTGCCATTCTGACCTGGCGCGTGAATCCACTCACAGAAGCTCTGGGGCTCTTCAACATTTTCCTGTATACCTGCTG
CTACACACCACTGAAGAGGATCAGCATTGCTAACACATGGGTCGGAGCCGTGGTTGGGGCCATCCCGCCTGTCATGGGCC
GGACAGTGGCCACGAGCACCCTCGATGTTGGCACGTTACTCCTGGGAGGAATCCTCTACTCCTGGCAGTTTCCTCATTTA
AACGCCCTGAGCTGGGGCCTCCGTGAAGACTACTCTCGGGGCGGCTACTGCATGACGTCGGTCACCCACCCGGGCCTGTG
CCAGCGCGTGGTGCTGTGCCACTGCCTGGCCCTGCTGGCGCTATCCATGGCAGCCCCCGTCCTGGAAATCACCACTTGGA
CTTTCGCCGTCATTGCCCTCCCCATCAATGCCTACATCTCCTACCTCTGCTTCCACTTCTACGTGAACGCAGACCGCAGG
AGCTGGCGGAGACTGTTCTTCTGCAGCCTGTGGCACCTGACGCTGCTGTTACTGCTCATGCTTACCTGCAAGCAGCGGTG
CGGGGCGGGGCGGGGGCCCCCTCCCAGC

Alignment

ORF - retro_cjac_3938 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.64 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLSSRLLTGWVGGCVWYLERRTIQESPHKFLHLVRNVNKQWITFQHFSFLRRMYVTQLNRSHNQQVKPKP
          T.SSRLLTG.VGGCVWYLER..IQ.SPHKFLHLVRNVN.QWITFQHFSFLRRMYVT.LNRSHNQQVKPKP
Retrocopy TFSSRLLTGCVGGCVWYLERIIIQVSPHKFLHLVRNVNEQWITFQHFSFLRRMYVTRLNRSHNQQVKPKP

Parental  EPVASTFLEKTSSGQAKAEIYEMRPLSPPSLSSSRKPNEKELIELELASEIEESIDVGKETKDEKQWKEM
          E.VASTFLEKTSSGQAKAEIYE.RPL.PPSLS.SRKPNEKELIELELASEIE..IDVGKETKDEKQ.KEM
Retrocopy EHVASTFLEKTSSGQAKAEIYETRPLLPPSLSLSRKPNEKELIELELASEIEDPIDVGKETKDEKQ*KEM

Parental  KLQVDDLPGILARLSKIKLTALVVSTTSAGFALAPGPFDFPCFLLTSIGTGLASCAANSINQFFEVPFDS
          K.QV.DLPGILA.LSKIK.T.LVVSTTSAGF.LA.GPFD.PCFLLTSIGTGL.SCAANSI..FFEVPFDS
Retrocopy KMQVSDLPGILAQLSKIKVTELVVSTTSAGFVLALGPFDLPCFLLTSIGTGLTSCAANSISRFFEVPFDS

Parental  NMNRTKNRPLVRGQISPLLAVSFATCCAVPGVAILTWGVNPLTGALGLFNIFLYTCCYTPLKRISIANTW
          NMNRTKNRP.VRG.ISPLLAVSFAT.CAVPGVAILTW.VNPLT.ALGLFNIFLYTCCYTPLKRISIANTW
Retrocopy NMNRTKNRPPVRGEISPLLAVSFAT*CAVPGVAILTWRVNPLTEALGLFNIFLYTCCYTPLKRISIANTW

Parental  VGAVVGAIPPVMGWTAATGSLDAGAFLLGGILYSWQFPHFNALSWGLREDYSRGGYCMMSVTHPGLCRRV
          VGAVVGAIPPVMG.T.AT..LD.G..LLGGILYSWQFPH.NALSWGLREDYSRGGYCM.SVTHPGLC.RV
Retrocopy VGAVVGAIPPVMGRTVATSTLDVGTLLLGGILYSWQFPHLNALSWGLREDYSRGGYCMTSVTHPGLCQRV

Parental  ALRHCLALLALSVAAPVLDITTWTFPVIALPINAYISYLGFRFYVDADRRSSRRLFFCSLWHLPLLLLLM
          .L.HCLALLALS.AAPVL.ITTWTF.VIALPINAYISYL.F.FYV.ADRRS.RRLFFCSLWHL.LLLLLM
Retrocopy VLCHCLALLALSMAAPVLEITTWTFAVIALPINAYISYLCFHFYVNADRRSWRRLFFCSLWHLTLLLLLM

Parental  LTCKQRRGGGDPGPPPS
          LTCKQR.G.G..GPPPS
Retrocopy LTCKQRCGAG-RGPPPS

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	4.93 RPM
SRP051959_heart	0.02 RPM	7.59 RPM
SRP051959_kidney	0.00 RPM	5.57 RPM
SRP051959_liver	0.02 RPM	3.16 RPM
SRP051959_lung	0.00 RPM	3.69 RPM
SRP051959_lymph_node	0.00 RPM	4.54 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.42 RPM
SRP051959_spleen	0.00 RPM	3.45 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3938 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3938 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3938 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015294	1 retrocopy	retro_btau_1425,
Canis familiaris	ENSCAFG00000017899	1 retrocopy	retro_cfam_1380,
Callithrix jacchus	ENSCJAG00000004522	1 retrocopy	retro_cjac_3938 ,
Felis catus	ENSFCAG00000010334	1 retrocopy	retro_fcat_814,
Otolemur garnettii	ENSOGAG00000007457	1 retrocopy	retro_ogar_606,