RetrogeneDB ID: retro_cjac_4227

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: Y:170056..171079(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023103
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CAB39
• Ensembl ID: ENSCJAG00000013349
• Aliases: None
• Description: calcium binding protein 39 [Source:HGNC Symbol;Acc:20292]

Sequence

>retro_cjac_4227
ATGCGGTTCCCGTTCGGGAAGTCTCACAAATCTCCAGCAGACACTGTGAAGGATCTGAAGGAAAGCATGGCCGTTCTGGA
AGAGCAAGACATTTCTGACAAAAAAGCAGAAAAGGCTACAGAAGAAGTTTCCAAAAATCTGGTTGCCATGAAAGAAATTC
TGTATGGCACAAATGAAAAAGAGCCTCAGACAGAAGCAGTGGCCCAGCTTGCTCACGAACTCTGTAATAGTGGGCTTCTT
AGCACCCTGGTAGCTGATTTACAGCTCGTTGACTTTGAGGGCAAAAAAGACGTGGCTCAAATTTTCAACAATGTTCTCAG
AAGACAAATTGGTACAAGAACTCCTACTGTTGAATACATCTGCACCCAACAGAATATTTTGTTCGTGTTATTGAAAGGGT
ATGAATCTCCAGAAATAGCTTTAAATTGTGGAATAATGTTAAGAGAATGCATCAGACATGAACCACTTGCAAAAATCATT
TTGTGGTCAGAACAGGTTTCTGATTTCTTCAGATATGTCGAAATGTCAACGTTTGACATAGCTTCAGATGCATTTGCCAC
ATTCAAGGATTTACTTACAAGACATAAATTGCTCAGTGCAGAATTTTTGGAACAGCATTATGATAGATTTTTGAGTGAAT
ATGAGAAGTTACTTCATTCAGAAAATTACGTGACAAAAAGAAAGTCACTCAAGCTTCTCGGTGAACTACTACTAGACAGA
CACAACTTCACAATTATGACAAAATACATCAGTAAACCTGAGAACCTCAAGTTAATGATGAACCTGCTGCGAGACAAAAG
TCGCAACATCCAGTTGGAGGCCTTTCACGTTTTTAAGGTGTTTGTAGCCAATCCTAACAAGACACAGCCCATCCTAGACA
TCCTCCTCAAGAACCAGACCAAACTCATAGAGTCCCTCAGCAAGTTTCAGAATGACAGGACGGAGGATGAGCAGTTTAAT
GACGAGAAGACCTATTTAGTTAAACAGATCAGGGATTTGAAGAGACCAGCTCAGCAAGAAGCT

Alignment

ORF - retro_cjac_4227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFPFGKSHKSPADIVKNLKESMAVLEKQDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQL
          M.FPFGKSHKSPAD.VK.LKESMAVLE.QDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQL
Retrocopy MRFPFGKSHKSPADTVKDLKESMAVLEEQDISDKKAEKATEEVSKNLVAMKEILYGTNEKEPQTEAVAQL

Parental  AQELYNSGLLSTLVADLQLIDFEGKKDVAQIFNNILRRQIGTRTPTVEYICTQQNILFMLLKGYESPEIA
          A.EL.NSGLLSTLVADLQL.DFEGKKDVAQIFNN.LRRQIGTRTPTVEYICTQQNILF.LLKGYESPEIA
Retrocopy AHELCNSGLLSTLVADLQLVDFEGKKDVAQIFNNVLRRQIGTRTPTVEYICTQQNILFVLLKGYESPEIA

Parental  LNCGIMLRECIRHEPLAKIILWSEQFYDFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRF
          LNCGIMLRECIRHEPLAKIILWSEQ..DFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRF
Retrocopy LNCGIMLRECIRHEPLAKIILWSEQVSDFFRYVEMSTFDIASDAFATFKDLLTRHKLLSAEFLEQHYDRF

Parental  FSEYEKLLHSENYVTKRQSLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQFEAFHVFKV
          .SEYEKLLHSENYVTKR.SLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQ.EAFHVFKV
Retrocopy LSEYEKLLHSENYVTKRKSLKLLGELLLDRHNFTIMTKYISKPENLKLMMNLLRDKSRNIQLEAFHVFKV

Parental  FVANPNKTQPILDILLKNQTKLIEFLSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA
          FVANPNKTQPILDILLKNQTKLIE.LSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA
Retrocopy FVANPNKTQPILDILLKNQTKLIESLSKFQNDRTEDEQFNDEKTYLVKQIRDLKRPAQQEA

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	0.27 RPM	35.37 RPM
SRP051959_heart	0.12 RPM	31.24 RPM
SRP051959_kidney	0.33 RPM	33.70 RPM
SRP051959_liver	0.09 RPM	18.37 RPM
SRP051959_lung	0.16 RPM	40.16 RPM
SRP051959_lymph_node	0.21 RPM	37.99 RPM
SRP051959_skeletal_muscle	0.22 RPM	32.69 RPM
SRP051959_spleen	0.11 RPM	36.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4227 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4227 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013349	1 retrocopy	retro_cjac_4227 ,
Equus caballus	ENSECAG00000015288	1 retrocopy	retro_ecab_288,
Otolemur garnettii	ENSOGAG00000002000	1 retrocopy	retro_ogar_1455,