RetrogeneDB ID: retro_cjac_2167

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:108052520..108053346(+)
• Located in intron of: ENSCJAG00000005621

Retrocopy information

• Ensembl ID: ENSCJAG00000010375
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OLFM1
• Ensembl ID: ENSCJAG00000005718
• Aliases: None
• Description: None

Sequence

>retro_cjac_2167
TCCAATCTTGAAAAAAGCCTCCATGCATGCATGCAAAAACTATCTTGCGGGAAGTTGACGGGCATCAGTGACCCCATGAC
AGTCAAGACCTCCGACTCTAGGTTCGGATCCTGGATGACAGACCCTCTCGCCCCAGAAGGCGATAACCGGCTGTGGTACA
TGGATGGCTATCAGAACAACCGCTTCGTGCGTGAGTACAAATCCATGGTGGACTTCATGAACACGGACAATTTCACCTCG
CACCACCTCCCCCACCCCTGGTCGGGCACGGGGGCAGGTGGTGTACAATGGGTCCATCTATTTCAACACGTTCCAGAGCC
ACATCATCATCAGGTTCGACCTGAAGACAGAGACCACCCTCAAGACCCGCAGCCTGGACTATGCCAGCTACAACATGTAC
CACTATGCCTGGGGCGTTCACTTGGACATCGACCTCATGGTGGACGAGAGCAGGCTGTGGGCCGTGTATGCCACCAACCA
GAACACCAGCAACATCGTGGTCAGCAGGCTGGACCCCGTGTCCCTGCAGACGCTGCAGACGTGGAACACGAGCTATTCCA
AGCGCAGCACCGGGGAGGCCTTCATCATCTGTGGCACACTGTATGTCACCAACGGCTACTCGGGGAGCACCAAGGTCCAC
TACGCCCACCAGACCAACGCCTCCACCTATGAGTCCCCTTCCATCGACGTCCCCTTCCAGAACAAATACTCCCACATCTC
CATGCTGGACTACAACCCCAAGGACTGCGCGCTGTACGCCTGGAACAATGGTCACCAGATCCTCTACAACATGACCCTCT
TCCACGTCATCCGCTCTGACGAGTTG

Alignment

ORF - retro_cjac_2167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.53 %
• Parental protein coverage: 56.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SNLEERLRACMQKLACGKLTGISDPVTVKTSGSRFGSWMTDPLAPEGDNRVWYMDGYHNNRFVREYKSMV
          SNLE..L.ACMQKL.CGKLTGISDP.TVKTS.SRFGSWMTDPLAPEGDNR.WYMDGY.NNRFVREYKSMV
Retrocopy SNLEKSLHACMQKLSCGKLTGISDPMTVKTSDSRFGSWMTDPLAPEGDNRLWYMDGYQNNRFVREYKSMV

Parental  DFMNTDNFTSHRLPHPWSGT-GQVVYNGSIYFNKFQSHIIIRFDLKTETILKTRSLDYAGYNNMYHYAWG
          DFMNTDNFTSH.LPHPWSGT.GQVVYNGSIYFN.FQSHIIIRFDLKTET.LKTRSLDYA.Y.NMYHYAWG
Retrocopy DFMNTDNFTSHHLPHPWSGT>GQVVYNGSIYFNTFQSHIIIRFDLKTETTLKTRSLDYASY-NMYHYAWG

Parental  GHSDIDLMVDESGLWAVYATNQNAGNIVVSRLDPVSLQTLQTWNTSYPKRSAGEAFIICGTLYVTNGYSG
          .H.DIDLMVDES.LWAVYATNQN..NIVVSRLDPVSLQTLQTWNTSY.KRS.GEAFIICGTLYVTNGYSG
Retrocopy VHLDIDLMVDESRLWAVYATNQNTSNIVVSRLDPVSLQTLQTWNTSYSKRSTGEAFIICGTLYVTNGYSG

Parental  GTKVHYAYQTNASTYE--YIDIPFQNKYSHISMLDYNPKDRALYAWNNGHQILYNVTLFHVIRSDEL
          .TKVHYA.QTNASTYE...ID.PFQNKYSHISMLDYNPKD.ALYAWNNGHQILYN.TLFHVIRSDEL
Retrocopy STKVHYAHQTNASTYESPSIDVPFQNKYSHISMLDYNPKDCALYAWNNGHQILYNMTLFHVIRSDEL

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	0.02 RPM	7.59 RPM
SRP051959_heart	0.02 RPM	2.93 RPM
SRP051959_kidney	0.02 RPM	2.53 RPM
SRP051959_liver	0.00 RPM	1.39 RPM
SRP051959_lung	0.00 RPM	1.66 RPM
SRP051959_lymph_node	0.00 RPM	5.25 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.90 RPM
SRP051959_spleen	0.00 RPM	1.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2167 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2167 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005718	1 retrocopy	retro_cjac_2167 ,