RetrogeneDB ID: retro_cjac_1186

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:14445797..14446331(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MED30
• Ensembl ID: ENSCJAG00000005824
• Aliases: None
• Description: mediator complex subunit 30 [Source:HGNC Symbol;Acc:23032]

Sequence

>retro_cjac_1186
ATGCCCACCCCTCCATGGGCCGCATCAGGAATGGCGCCCGGGCCCTTTGCCCGGCCCCAGGCTCAGCAGGCTGCCCGGGA
GGTGAACACGGCGTCGCTGTGCCGCATCGGGCAGGAGACGGTGACGGACATCGTGTGCCGCACCCTAGAGATCTTCCAGC
TCCTCAGGAATATGCAGCTGCCAAATGGTGTCACTTCCCACACTGGAACGTATCAAGACCGGTTAACGAAGCTACAGGAT
AATCTTCGCCAACTTTCAGTTCTCTTCAGGAAGCTGAGATTGGTATATGACAAGTGCAATGAAAACTGTGGAGGGATGGA
TCCCATTCCAGTAGAGCAACTTATTCCATATGTGAAAGAAGATGGCTCAAAGAATGATGATCGGGCTGGCCCACCTCGTT
TTGCTAGTGAGGAGAGGCGAGAAATTGCTGAAGTAAATAAGAAACTCAAACAGAAGAATCAACAGCTGAAGCAAATTATG
GATCAATTACAAAATCTCATCTGGGATATAAATGCCATGTTGGCAATGAGGAAC

Alignment

ORF - retro_cjac_1186 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQDKLPNGVTYHT
          M.TPP.AASGMAPGPFA.PQAQQAAREVNTASLCRIGQETV.DIV.RT.EIFQLLRNMQ..LPNGVT.HT
Retrocopy MPTPPWAASGMAPGPFARPQAQQAAREVNTASLCRIGQETVTDIVCRTLEIFQLLRNMQ--LPNGVTSHT

Parental  GTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEEDGSKNDDRAGPPRFASEE
          GTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYV.EDGSKNDDRAGPPRFASEE
Retrocopy GTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVKEDGSKNDDRAGPPRFASEE

Parental  RREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
          RREIAEVNKKLKQKNQQLKQIMDQL.NLIWDINAMLAMRN
Retrocopy RREIAEVNKKLKQKNQQLKQIMDQLQNLIWDINAMLAMRN

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	0.09 RPM	2.29 RPM
SRP051959_heart	0.02 RPM	3.88 RPM
SRP051959_kidney	0.95 RPM	2.51 RPM
SRP051959_liver	0.76 RPM	3.14 RPM
SRP051959_lung	0.28 RPM	4.91 RPM
SRP051959_lymph_node	0.00 RPM	3.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.49 RPM
SRP051959_spleen	0.04 RPM	3.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1186 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1186 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005824	1 retrocopy	retro_cjac_1186 ,
Sorex araneus	ENSSARG00000000870	2 retrocopies	retro_sara_332, retro_sara_455,
Tarsius syrichta	ENSTSYG00000009760	2 retrocopies	retro_tsyr_1855, retro_tsyr_22,