RetrogeneDB ID: retro_cjac_222

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:16216551..16217913(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022035
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSCJAG00000009116
• Aliases: None
• Description: None

Sequence

>retro_cjac_222
ATGAAGCTACTAACCAGAGCCGGATCCTTCTCGAGATTTTATTCTCTCAAAGTTGCCCCCAAAGTTAAAGCCACAGCTGC
GCCTGCAGGAGCACTGCCACAACCTCAGGACCTCGAGTTTACCAAGTTACCAAATGGTTTGGTGATTGCTTCTTTGGAAA
ACTATGCTCCTGTATCAAGAATTGGGTTGTTCATTAAAGCAGGCAGTAGATATGAGGACTCCAACAATTTAGGAACCACT
CATTTGCTGCGTCTTGCATCCGGTCTGACGACAAAAGGAGCTTCATCTTTCAAGATAACCCGTGGAATTGAAGCAGTTGG
TGGCTTATTAAGTGTGACTGCAACAAGGGAAAACATGGCTTACACTGTGGAATGCCTGCGGGGCGATGTTGATATTCTAA
TGGAGTTCCTGCTCAATGTCACCACATCACCAGAATTTCGTCACTGGGAAGTAGGTGAGATTCAGCCTCAGCTAAAGATT
GACAAGGCTGTGGCCTTTCAGAATCCACAGACTCATGTCATTGAAAATTTGCATGCAGCAGCTTACCGGAATGCCTTGGC
TAATCCCTTGTATTGCCCTGACTATAGGATTGGAAAAGTGACACCAGAGGAGTTACATTACTTCGTTCAGAACCATTTCA
CAAGTGCAAGAATGGCTTTGATTGGACTTGGTGTGAGTCATCCTGTTCTAAAGCAAGTTGCTGAACAGTTTCTCAACATG
AGAGGTGGACTTGGTTTATCTGGTGCCAAGGCCAAGTACTGTGGAGGCGAAATCCGAGAACAGAATGGGGACAGTCTTGT
CCATGCCGCTCTTGTAGCAGAAAGTGCTGCCGCGGGAAGTGCAGAGGCAAATGCATTTAGTGTTCTTCAGCATGTCCTCG
GTGCTGGGCCACATATCAAGAGGGGCAGCAACACCACCAGCCATCTGCACCAGGCTGTTACCAAGGCAACTCACCAGCCA
TTCGATGTTTCTGCATTTAATGCCAGTTACTCAGATTCTGGACTCTTTGGGATTTATACTATCTCCCAGGCCACAGCTGC
TGGAGATGTTATCAAGGCTGCCTATAATCAAGTAAAAACAATTGCTCAAGGAAACCTTTCCAACACAGATGTCCAAACTG
CCAAGAACAAGCTGAAAGCTGGATACCTAATGTCAGTGGAGTCTTCTGAGAGTCTCCTGGAAGAAGTCGGGTCCCAGGCC
CTAATTGCTGGTTCTTACGTGCCACCATCCACAGTCCTTCAGCAGATTGATTCAGTGGCTAACGCTGATATCATAAATGC
GGCAAAGAAGTTTGTTTCTGGCAAAAAGTCGATGGCAGAAAGTGGAAATTTGGGACATACGCCTTTTGTTGATGAGTTGT
AA

Alignment

ORF - retro_cjac_222 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLLTRAGSFSRFYSLKVAPKVKATAAPAGAPPQPQDLEFTKLPNGLVIASLENYAPVSRIGLFIKAGSR
          MKLLTRAGSFSRFYSLKVAPKVKATAAPAGA.PQPQDLEFTKLPNGLVIASLENYAPVSRIGLFIKAGSR
Retrocopy MKLLTRAGSFSRFYSLKVAPKVKATAAPAGALPQPQDLEFTKLPNGLVIASLENYAPVSRIGLFIKAGSR

Parental  YEDSNNLGTTHLLRLASGLTTKGASSFKITRGIEAVGGLLSVTATRENMAYTVECLRGDVDILMEFLLNV
          YEDSNNLGTTHLLRLASGLTTKGASSFKITRGIEAVGGLLSVTATRENMAYTVECLRGDVDILMEFLLNV
Retrocopy YEDSNNLGTTHLLRLASGLTTKGASSFKITRGIEAVGGLLSVTATRENMAYTVECLRGDVDILMEFLLNV

Parental  TTSPEFRHWEVGEIQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTPEELHYFVQ
          TTSPEFRHWEVGEIQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTPEELHYFVQ
Retrocopy TTSPEFRHWEVGEIQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTPEELHYFVQ

Parental  NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGLGLSGAKAKYRGGEIREQNGDSLVHAALVAESAAAGS
          NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGLGLSGAKAKY.GGEIREQNGDSLVHAALVAESAAAGS
Retrocopy NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGLGLSGAKAKYCGGEIREQNGDSLVHAALVAESAAAGS

Parental  AEANAFSVLQHVLGAGPHIKRGSNTTSHLHQAVTKATHQPFDVSAFNASYSDSGLFGIYTISQATAAGDV
          AEANAFSVLQHVLGAGPHIKRGSNTTSHLHQAVTKATHQPFDVSAFNASYSDSGLFGIYTISQATAAGDV
Retrocopy AEANAFSVLQHVLGAGPHIKRGSNTTSHLHQAVTKATHQPFDVSAFNASYSDSGLFGIYTISQATAAGDV

Parental  IKAAYNQVKTIAQGNLSNTDVQTAKNKLKAGYLMSVESSEGLLEEVGSQALIAGSYVPPSTVLQQIDSVA
          IKAAYNQVKTIAQGNLSNTDVQTAKNKLKAGYLMSVESSE.LLEEVGSQALIAGSYVPPSTVLQQIDSVA
Retrocopy IKAAYNQVKTIAQGNLSNTDVQTAKNKLKAGYLMSVESSESLLEEVGSQALIAGSYVPPSTVLQQIDSVA

Parental  NADIINAAKKFVSGKKSMAASGNLGHTPFVDEL
          NADIINAAKKFVSGKKSMA.SGNLGHTPFVDEL
Retrocopy NADIINAAKKFVSGKKSMAESGNLGHTPFVDEL

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	0.22 RPM	50.34 RPM
SRP051959_heart	0.23 RPM	118.05 RPM
SRP051959_kidney	0.51 RPM	82.82 RPM
SRP051959_liver	0.28 RPM	100.57 RPM
SRP051959_lung	0.18 RPM	30.50 RPM
SRP051959_lymph_node	0.05 RPM	27.94 RPM
SRP051959_skeletal_muscle	0.57 RPM	134.61 RPM
SRP051959_spleen	0.19 RPM	35.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_222 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_222 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222 ,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,