RetrogeneDB ID: retro_cjac_3937

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286332.1:10091..10761(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009256
• Aliases: None
• Description: None

Sequence

>retro_cjac_3937
ATGCTGGCAATTTCAAGAAACCAAAAGTTGTTACAGTCTGGAGAAGAAAACCAGGTCCTGGAATTGTTAACTCATTGAGA
TAGGGAATTTCAAGGACTAATGAAATTGGCAGTTAGTCAGGGGAAAATTCATCATGAAATGCAAGTTTTGGAAAAAGAAG
TAGAGAAGAGAGACAGTGATATTCGGCAACTACAAAAACAGCTAAAGGAAGCAGAACAAATACTGGCAGGAGCTGTTTAC
CAAGCAAAGGAGAAACTCAAGTCCATAGAAAAAGCAAGAAAAGGCGCTATCTCCTCTGAAGAAATAATGAAGTATGCACA
TAGGATCAGTGCAAGTAATGCTGTGTGTGCTCCACTAACCTTGGTTCCAGGGGACCCCGGAGACCTTAACCAACTGATTT
AGAGATGAGAAGTGGTTTACTGGGTCAGATGAACAATCCTTCCACTAATGGTGTGAATGGCCATTTACCAGGGGATGCAC
TCGCAGCAGGAAGATTGCCAGATGTCCTTGCTCCTAAGTATCCATGGCAGTCGAATGACATGTCAATGAATATGTTACCA
CCAAATCATAGCATTGACTTTTTGCGGAACCTCCTGGGCATAATAAAGAAAATGAAGATGATGTAGAGATTATGTCAATG
GACTCCTCAAGCAGTAGTAGTGAGCCTGAT

Alignment

ORF - retro_cjac_3937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLAISRNQKLLQAGEENQVLELLIHRDGEFQELMKLAVNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKE
          MLAISRNQKLLQ.GEENQVLELL.H.D.EFQ.LMKLAV.QGKIHHEMQVLEKEVEKRDSDI.QLQKQLKE
Retrocopy MLAISRNQKLLQSGEENQVLELLTH*DREFQGLMKLAVSQGKIHHEMQVLEKEVEKRDSDIRQLQKQLKE

Parental  AEQILATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVPGD-PRRPYPTDLEMRSG
          AEQILA.AVYQAKEKLKSIEKARKGAISSEEI.KYAHRISASNAVCAPLT.VPGD.PRRP.PTDLEMRSG
Retrocopy AEQILAGAVYQAKEKLKSIEKARKGAISSEEIMKYAHRISASNAVCAPLTLVPGD<PRRP*PTDLEMRSG

Parental  LLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSNDMAMNMLPPNHSSDFL-LEPPGHNKENEDD
          LLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAP.YPWQSNDM.MNMLPPNHS.DFL..EPPGHNKENEDD
Retrocopy LLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPKYPWQSNDMSMNMLPPNHSIDFL<AEPPGHNKENEDD

Parental  VEIMSTDSSSSSSESD
          VEIMS.DSSSSSSE.D
Retrocopy VEIMSMDSSSSSSEPD

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	4.26 RPM
SRP051959_heart	0.00 RPM	5.93 RPM
SRP051959_kidney	0.02 RPM	5.81 RPM
SRP051959_liver	0.06 RPM	6.00 RPM
SRP051959_lung	0.00 RPM	6.15 RPM
SRP051959_lymph_node	0.07 RPM	5.87 RPM
SRP051959_skeletal_muscle	0.02 RPM	3.52 RPM
SRP051959_spleen	0.04 RPM	6.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3937 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3937 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937 ,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292,