RetrogeneDB ID: retro_cjac_1340

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:49332447..49333565(+)
• Located in intron of: ENSCJAG00000015146

Retrocopy information

• Ensembl ID: ENSCJAG00000015152
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MECR
• Ensembl ID: ENSCJAG00000009994
• Aliases: None
• Description: None

Sequence

>retro_cjac_1340
ATGTGGGTCTGCAGCACGCTGTGGCGGGTGCGAACCCTCGCCTGGCTGTGGCGGAGGCTGCTCCCTGCTTCTGGCTGTCA
CGGACCTGCCGCCTCCTACTACTCCTCATCCACCGAGCCTGCCCGGGTCCCGGCACTTGTCTATGGGCACCACGGGGATC
CCGCCAAGGTCGTCGAACTGAAGAACCTGGAGCTAGCTGCTGTGGGAGGATCAGACGTCCTCATGAAGATGCTGGCGGCC
CCTATCAATCCATCTGACATAAATATGATCCAAGGAAACTACAGCCTCCTTCCCGAACTGCCTGCTGTTGGAGGGAATGA
AGGTGTTGCCCAGGTGTTAGCAGTGGGCAGCAGTGTGACGAGGCTCAAGCCAGGAGACTGGGTGATTCCTGCAAATGCTG
GTTTGGGAACCTGGCGGACTGAGGCCATGTTCAGTGAGGAAGCACTGATCCAAGTTCCAAGTGACATCCCTCTTGAGAGC
GCTGCCACCCTGGGTGTCAATCCCTGCACAGCCTACAGGATGTTGATGGACTTTGAGCAGCTGCAGCCAGGGGATTCTGT
CATCCAGAATGCATCCAACAGTGGAGTGGGCCAAGCGGTCATCCAGATCGCGGCAGCCCTGGGCCTGAGAACGATCAATG
TGGTCCAAGACAGACCTGATATCCAGAAGCTGACTGACAGACTGAAGAGTCTGGGGGCCAAGCATGTCATCACAGAAGAG
GAGCTAAGAAGGCCCGAAATAAAAAACTTGTTTAAGGACATGCCCCAGCCACACCTTGCTCTCAACTGTGTTGGTGGGAA
AAGCTCCACAGAGCTGCTGCGGCAGTTAGCGCGTGGAGGAACCATGGTAACCTATGGGGGAATGGCCAAGCAGCCCATCA
TAGCCTCTGTGAGCCTGCTCATTTTTAAGGATCTCAAACTTCGGGGCTTTTGGTTGTCCCAGTGGAAGAAGGATCACAGT
CCAGACCAGTTCAAGGAGCTGATCCTCACACTGTGCGATCTCATCCGCCAAGGCCAGCTCACAGCCCTGCCTGCTCCCAG
GTCCCGCTGCAGGACTACCAGCATGCCTTGGAAGCCTCCATGAAGCCCTTTGTGTCTTCAAAGCAGATTCTCACCATG

Alignment

ORF - retro_cjac_1340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MWVCSTLWRVRT-PPGC-GG-LIPASGCHGPAASNYSASAEPARVPALVYGHHGDPAKVVELKNLELAAV
          MWVCSTLWRVRT..PGC.GG.L.PASGCHGPAAS.YS.S.EPARVPALVYGHHGDPAKVVELKNLELAAV
Retrocopy MWVCSTLWRVRT>SPGCGGG<LLPASGCHGPAASYYSSSTEPARVPALVYGHHGDPAKVVELKNLELAAV

Parental  GGSDVLVKMLAAPINPSDINMIQGNYGLLPELPAVGGNEGVAQVVAVGSSVTRLKPGDWVIPANAGLGTW
          GGSDVL.KMLAAPINPSDINMIQGNY.LLPELPAVGGNEGVAQV.AVGSSVTRLKPGDWVIPANAGLGTW
Retrocopy GGSDVLMKMLAAPINPSDINMIQGNYSLLPELPAVGGNEGVAQVLAVGSSVTRLKPGDWVIPANAGLGTW

Parental  RTEAVFSEEALIQVPSDIPLESAATLGVNPCTAYRMLMDFEQLQPGDSVIQNASNSGVGQAVIQIAAALG
          RTEA.FSEEALIQVPSDIPLESAATLGVNPCTAYRMLMDFEQLQPGDSVIQNASNSGVGQAVIQIAAALG
Retrocopy RTEAMFSEEALIQVPSDIPLESAATLGVNPCTAYRMLMDFEQLQPGDSVIQNASNSGVGQAVIQIAAALG

Parental  LRTINVVRDRPDIQKLTDRLKSLGAKHVITEEELRRPEIKNLFKDMPQPRLALNCVGGKSSTELLRQLAR
          LRTINVV.DRPDIQKLTDRLKSLGAKHVITEEELRRPEIKNLFKDMPQP.LALNCVGGKSSTELLRQLAR
Retrocopy LRTINVVQDRPDIQKLTDRLKSLGAKHVITEEELRRPEIKNLFKDMPQPHLALNCVGGKSSTELLRQLAR

Parental  GGTMVTYGGMAKQPVIASVSLLIFKDLKLRGFWLSQWKKDHSPDQFKELILTLCDLIRQGQLTA-PACSQ
          GGTMVTYGGMAKQP.IASVSLLIFKDLKLRGFWLSQWKKDHSPDQFKELILTLCDLIRQGQLTA.PACSQ
Retrocopy GGTMVTYGGMAKQPIIASVSLLIFKDLKLRGFWLSQWKKDHSPDQFKELILTLCDLIRQGQLTA<PACSQ

Parental  VPLQDYQHALEASMKPFVSSKQILTM
          VPLQDYQHALEASMKPFVSSKQILTM
Retrocopy VPLQDYQHALEASMKPFVSSKQILTM

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	0.16 RPM	4.64 RPM
SRP051959_heart	0.21 RPM	7.45 RPM
SRP051959_kidney	0.04 RPM	8.05 RPM
SRP051959_liver	0.22 RPM	11.16 RPM
SRP051959_lung	0.28 RPM	5.51 RPM
SRP051959_lymph_node	0.09 RPM	8.49 RPM
SRP051959_skeletal_muscle	0.24 RPM	11.73 RPM
SRP051959_spleen	0.15 RPM	6.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1340 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1340 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	ENSCJAG00000009994	1 retrocopy	retro_cjac_1340 ,