RetrogeneDB ID: retro_cjac_4013

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288339.1:3437..4206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METT11D1
• Ensembl ID: ENSCJAG00000009609
• Aliases: METTL17, METT11D1
• Description: None

Sequence

>retro_cjac_4013
ACTACCTACCATTGGCAAGAACTGAGCTACAGTGAGGGACTGAGCCTGGTGTATATGGCAGCAAGACTGGATGGTGGCTT
TGCAGCAGTCTCCAGAGCATTCCATGAGATCCAGGCTCAAAATCAAGCATTTCAGCCACAAACTTTAATGGACTTTGGCT
CGGGTACTGGTTCTGTCACCTGGGCTGCTCACAGTGTTTGGGGTCAGACCCTACGTGAATATATGTGTGTGGACAGATCA
ACTGCCATGTTGGTTTTGGCAGAAAAGCTACTGAAAGGTGGTTCAGAATCTGGGGAGCCTTATATTCCAGGGGTATTTTT
CAGACAGTTTCTACCTGTATCACCCAAGGTGCAGTTTGATATAGTCATATCAGCCTTTTCCTTAAGTGAACTGCCCAGCA
AGGCTGACCGTAATGAAGTAGTTCAAACCTTATGGCGTAAGACACATCATTTCCTGGTGCTGGTGGAGAATGGAACAAAA
GCTGGGCACAGCCTTCTCATGGATGCCAGGGATCTGGTCCTTAACGGAAATGAGAAGTCACCTTTGGACCCTCCACCTGG
TTTTGTCTTTGCCCCATGTCCCCATGAACTCCCTTGTCCCCAGTTGACAACCTCTAAGCCCCTGGCTTGTAGCATCTCAC
AGGCGTACCATCCCATCCCCTTCAGCTGGAACAAGAAACCAAAGGAAGAAAAGTTCTCTTTGGTGATCCTTGCTTGGTGG
TCTCCAGATGAGGCTAATCACTGGGCCCCGTATCACTCAACCTGTCCTT

Alignment

ORF - retro_cjac_4013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 55.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTYHWQELSYSEGLSLVYMAARLDGGFAAVSRAFHEIQAQNQAFQPQTLMDFGSGTGSVTWAAHSVWGQT
          TTYHWQELSYSEGLSLVYMAARLDGGFAAVSRAFHEIQAQNQAFQPQTLMDFGSGTGSVTWAAHSVWGQT
Retrocopy TTYHWQELSYSEGLSLVYMAARLDGGFAAVSRAFHEIQAQNQAFQPQTLMDFGSGTGSVTWAAHSVWGQT

Parental  LREYMCVDRSTAMLVLAEKLLKGGSESGEPYIPGVFFRQFLPVSPKVQFDIVVSAFSLSELPSKADRNEV
          LREYMCVDRSTAMLVLAEKLLKGGSESGEPYIPGVFFRQFLPVSPKVQFDIV.SAFSLSELPSKADRNEV
Retrocopy LREYMCVDRSTAMLVLAEKLLKGGSESGEPYIPGVFFRQFLPVSPKVQFDIVISAFSLSELPSKADRNEV

Parental  VQTLWRKTHHFLVLVENGTKAGHSLLMDARDLVLNGNEKSPLDPRPGFVFAPCPHELPCPQLTTSKPLAC
          VQTLWRKTHHFLVLVENGTKAGHSLLMDARDLVLNGNEKSPLDP.PGFVFAPCPHELPCPQLTTSKPLAC
Retrocopy VQTLWRKTHHFLVLVENGTKAGHSLLMDARDLVLNGNEKSPLDPPPGFVFAPCPHELPCPQLTTSKPLAC

Parental  SISQAYHPIPFSWNKKPKEEKFSLVILARGSPEEANRW-PRITQPVL
          SISQAYHPIPFSWNKKPKEEKFSLVILA..SP.EAN.W.PRITQPVL
Retrocopy SISQAYHPIPFSWNKKPKEEKFSLVILAWWSPDEANHW>PRITQPVL

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	0.04 RPM	5.68 RPM
SRP051959_heart	0.02 RPM	6.49 RPM
SRP051959_kidney	0.00 RPM	9.96 RPM
SRP051959_liver	0.00 RPM	6.89 RPM
SRP051959_lung	0.00 RPM	10.44 RPM
SRP051959_lymph_node	0.02 RPM	12.56 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.94 RPM
SRP051959_spleen	0.00 RPM	10.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4013 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4013 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4013 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	ENSCJAG00000009609	1 retrocopy	retro_cjac_4013 ,