RetrogeneDB ID: retro_cjac_40

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:89846384..89847575(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022933
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MRPS9
• Ensembl ID: ENSCJAG00000008156
• Aliases: None
• Description: None

Sequence

>retro_cjac_40
ATGGCGGCCCCCTGTGTGTCCTATTGCGGAGCAGTTTCCTGCCGGCTGCTTCTCTGGGGTAGGGGTAGCCTCCTCCGGAA
GCAAGTCCTCTGGAAAACCGCGGCAGCTGAGTTGCAAACAAATGTCAGATCCCAGATATCAGGGCAAAGTCATACTGCAG
TTGCAACAAGAAAGAAAAATGTTCCCGCCTTAAAACGTGAAACTTACACAGTGGATTTTATTAAAAAGCAGATTGAAGAG
TTCAACATAGGAAAGAGACATTTAGCCAACATGATGGGAGAAGATCCAGAAAGTTTCACTCAAGAGGATATTGATAAAGC
TATTGCTTACCTTTTCCCAAGTGGTTTGTTTGAGAAAGAAGCCAGGCCAATAATGAAGCATCCTGAACTGATTTTTCCAA
AACAAAGAGCAATCCAGTGGGGAGAAGATGGCCGTCCATTTCACTATCTCTTCTATACTGGCAAACAGTCGTACTATTCA
TTAATGCATGATGTATACGGAATGTTACTCAATGTAGAAAAACGTCAAAGTCAGTTGCAAGCCAAAGGCCTCCTTCCAGA
AGAAACTAAAACCAGAGACCTGATTGGCAGCAGATGGCTGATTAAGGAGGAACTAGAAGAAATGTTAGTGGAAAAACTGT
CAGATCAAGATTATATGCAGTTCATTCACCTGCTAGAAAAGTTATTGACATTGCAATATGGTGCTGCTGAGGAAGAATTT
GTGCAGAGGTTTCGAAGAAGTGTAATCATTCAATCAAAAAAACAGCTGATTGAACCTGTGCAGTATGATGAGCAAGGAAT
GGCCTTTAGCAAAAGCGAAGGTAAAAGAAAGACTGCAAAAGCAGAAGCAATTGTTTATGAACATGGAAGTGGAAGAATAA
AAGTAAATGGAATTGATTACCTGCATTACTTCCCAATCATGCAGGACAGAGAACAGCTGATGTTCCCTTTCCACTTCGTT
GACCGGCTTGGGAAACACGATGTGACCTGCACAGTCTCAGGGGGCGGGAGGTCGGCACAGGTTGGAGCAGTACGACTGGC
AATGGCAAAAGCCTTGTGCAGCTTTCTCACTGAGGACGAGGTCGAATGGATGAGACAAGCTGGACTGCTTACTACTGATC
CACGTGTGAGAGAACGGAAGAAGCCAGGCCAAGAGGGAGCCCGCAGAAAGTTTACCTGGAAGAAGCGCTAA

Alignment

ORF - retro_cjac_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPCVSYCGAVSCRLLLWGRGSLLRKQVLWKTAAAELQTNVRSQISGQSHTAVATRKKNVPALKHETYT
          MAAPCVSYCGAVSCRLLLWGRGSLLRKQVLWKTAAAELQTNVRSQISGQSHTAVATRKKNVPALK.ETYT
Retrocopy MAAPCVSYCGAVSCRLLLWGRGSLLRKQVLWKTAAAELQTNVRSQISGQSHTAVATRKKNVPALKRETYT

Parental  VDFIKKQIEEFNIGKRHLANMMGEDPESFTQEDIDKAIAYLFPSGLFEKEARPIMKHPELIFPKQRAIQW
          VDFIKKQIEEFNIGKRHLANMMGEDPESFTQEDIDKAIAYLFPSGLFEKEARPIMKHPELIFPKQRAIQW
Retrocopy VDFIKKQIEEFNIGKRHLANMMGEDPESFTQEDIDKAIAYLFPSGLFEKEARPIMKHPELIFPKQRAIQW

Parental  GEDGRPFHYLFYTGKQSYYSLMHDVYGMLLSVEKRQSQLQAKGLLPEETKTRDLIGSRWLIKEELEEMLV
          GEDGRPFHYLFYTGKQSYYSLMHDVYGMLL.VEKRQSQLQAKGLLPEETKTRDLIGSRWLIKEELEEMLV
Retrocopy GEDGRPFHYLFYTGKQSYYSLMHDVYGMLLNVEKRQSQLQAKGLLPEETKTRDLIGSRWLIKEELEEMLV

Parental  EKLSDQDYMQFIHLLEKLLTLQYGAAEEEFVQRFRRSVIIQSKKQLIEPVQYDEQGMAFSKSEGKRKTAK
          EKLSDQDYMQFIHLLEKLLTLQYGAAEEEFVQRFRRSVIIQSKKQLIEPVQYDEQGMAFSKSEGKRKTAK
Retrocopy EKLSDQDYMQFIHLLEKLLTLQYGAAEEEFVQRFRRSVIIQSKKQLIEPVQYDEQGMAFSKSEGKRKTAK

Parental  AEAIVYEHGSGRIKVNGIDYLHYFPIMQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQAGAVRLAMAK
          AEAIVYEHGSGRIKVNGIDYLHYFPIMQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQ.GAVRLAMAK
Retrocopy AEAIVYEHGSGRIKVNGIDYLHYFPIMQDREQLMFPFHFVDRLGKHDVTCTVSGGGRSAQVGAVRLAMAK

Parental  ALCSFLTEDEVEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR
          ALCSFLTEDEVEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR
Retrocopy ALCSFLTEDEVEWMRQAGLLTTDPRVRERKKPGQEGARRKFTWKKR

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	0.11 RPM	11.60 RPM
SRP051959_heart	0.23 RPM	18.33 RPM
SRP051959_kidney	0.18 RPM	16.37 RPM
SRP051959_liver	0.06 RPM	11.74 RPM
SRP051959_lung	0.15 RPM	15.71 RPM
SRP051959_lymph_node	0.14 RPM	14.15 RPM
SRP051959_skeletal_muscle	0.09 RPM	14.96 RPM
SRP051959_spleen	0.17 RPM	13.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_40 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_40 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_40 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002122	1 retrocopy	retro_cfam_519,
Callithrix jacchus	ENSCJAG00000008156	1 retrocopy	retro_cjac_40 ,
Otolemur garnettii	ENSOGAG00000007255	1 retrocopy	retro_ogar_3314,
Pteropus vampyrus	ENSPVAG00000000927	1 retrocopy	retro_pvam_963,