RetrogeneDB ID: retro_cjac_2323

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:31954535..31955677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCD2
• Ensembl ID: ENSCJAG00000019528
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [Source:HGNC Symbol;Acc:11107]

Sequence

>retro_cjac_2323
CAACGAATCCGGGAGCTTGTCCCAGAGTCTCAGGCCTACATGGATCTCTTGGCTTTTGAGCGGAAGCTGGACCAGACCAT
TGCTCGCAAACGAATGGAGATCCAGGAGGCCATCAAAAAGCCTCTGACACAAAAGCGAAAGCTTCGGATCTACATTTCCA
ACACATTCAGTCCCAGCAAGGCAGAAGGCGACAGTGTAGGAACTGCAGGGACCCCTGGGGGAACCCCAGCAGGGGACAAG
GTGGCTTCCTGGGAACTCCGAGTGGAAGGAAAACTGCTGGATGATCCTAGCAAACGGAAGTGGAAGTTTTCTTCATTCTT
TAAGAGCCTGGTCATTGAGCTGTATGGGCCTGACAATCACCTGGTGGAGTGGCACCGGATGCCCACCACCCAGGGGACAG
ATGGCTTCCAGGTAAAACGGCCTGGAGACCTCAATGTCAAGTGCACCCTCCTGCTCGTGCTGGATCATCAGCCTCCCCAA
TACAAATTGGACCCCCAATTGGCAAGACTGCTGGGAGTGCACACGCAGACGAGGGCTGCCATCATGCAGGCCCTGTGGCT
TTACATCAAGCATAACCAGCTGCAGGACGGGCACAGCAGGAGTACATCAACTGCAACCGCTATTTCCGCCAGATCTTCAG
TTGTGGCCCACTCGGTTTCTCTGAGATTCCCATGAAGCTGGCGGGGTTGCTGCAGCACCCGGACCCCATTGTCATCAATC
ATGTCATTAGTGTGGACCCAAACGACCAGAAGAAGACAGCCTGTTACGACATTGATGTGGAGGTGGACGACCCGCTGAAG
GCCCAGATGAGCAATTTTCTGGCCTCTACCACCAATCAGCAGGAGATTGCCTCCCTTGATGTCAAGATCCATGAGACCAT
TGAGTCCATCAACCAGCTAAAGACCCAGAGGGATTTCATGCTCAGCTTTAGCACTGACCCCTAGGACTTCATCCAGGAAT
GGCTCCGTTCCCAGCGCCGAGACCTCAAGATCATCACTGATGTGATTGGAAATCCTGAGGAGGAGAGATGAGCTGCTTTC
TACCACCAGCCCTGGGCCCAGGAAGCAGTAGGCAGGCACATCTTTGCCAAGGTGCAGCAGCGAAGGCAGGAACTGGAACA
GGTGCTAGGAATTCACCTGACC

Alignment

ORF - retro_cjac_2323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 80.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRIRELVPESQAYMDLLAFERKLDQTIARKRMEIQEAIKKPLTQKRKLRIYISNTFSPSKAEGDSVGTAG
          QRIRELVPESQAYMDLLAFERKLDQTIARKRMEIQEAIKKPLTQKRKLRIYISNTFSPSKAEGDSVGTAG
Retrocopy QRIRELVPESQAYMDLLAFERKLDQTIARKRMEIQEAIKKPLTQKRKLRIYISNTFSPSKAEGDSVGTAG

Parental  TPGGTPAGDKVASWELRVEGKLLDDPSKQKRKFSSFFKSLVIELDKELYGPDNHLVEWHRMPTTQETDGF
          TPGGTPAGDKVASWELRVEGKLLDDPSK.K.KFSSFFKSLVI....ELYGPDNHLVEWHRMPTTQ.TDGF
Retrocopy TPGGTPAGDKVASWELRVEGKLLDDPSKRKWKFSSFFKSLVI----ELYGPDNHLVEWHRMPTTQGTDGF

Parental  QVKRPGDLNVKCTLLLMLDHQPPQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHER-EYINC
          QVKRPGDLNVKCTLLL.LDHQPPQYKLDP.LARLLGVHTQTRAAIMQALWLYIKHNQLQDGH.R.EYINC
Retrocopy QVKRPGDLNVKCTLLLVLDHQPPQYKLDPQLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHSR<EYINC

Parental  NRYFRQIFSCGRLRFSEIPMKLAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPLKAQMSNFLA
          NRYFRQIFSCG.L.FSEIPMKLAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPLKAQMSNFLA
Retrocopy NRYFRQIFSCGPLGFSEIPMKLAGLLQHPDPIVINHVISVDPNDQKKTACYDIDVEVDDPLKAQMSNFLA

Parental  STTNQQEIASLDVKIHETIESINQLKTQRDFMLSFSTDPQDFIQEWLRSQRRDLKIITDVIGNPEEERRA
          STTNQQEIASLDVKIHETIESINQLKTQRDFMLSFSTDP.DFIQEWLRSQRRDLKIITDVIGNPEEER.A
Retrocopy STTNQQEIASLDVKIHETIESINQLKTQRDFMLSFSTDP*DFIQEWLRSQRRDLKIITDVIGNPEEER*A

Parental  AFYHQPWAQEAVGRHIFAKVQQRRQELEQVLGIRLT
          AFYHQPWAQEAVGRHIFAKVQQRRQELEQVLGI.LT
Retrocopy AFYHQPWAQEAVGRHIFAKVQQRRQELEQVLGIHLT

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	22.19 RPM
SRP051959_heart	0.23 RPM	15.14 RPM
SRP051959_kidney	0.07 RPM	21.88 RPM
SRP051959_liver	0.17 RPM	22.74 RPM
SRP051959_lung	0.41 RPM	26.55 RPM
SRP051959_lymph_node	0.09 RPM	23.06 RPM
SRP051959_skeletal_muscle	0.22 RPM	10.96 RPM
SRP051959_spleen	0.23 RPM	20.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2323 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2323 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2323 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012708	1 retrocopy	retro_cfam_256,
Callithrix jacchus	ENSCJAG00000019528	1 retrocopy	retro_cjac_2323 ,
Mustela putorius furo	ENSMPUG00000014835	1 retrocopy	retro_mputfur_89,
Sarcophilus harrisii	ENSSHAG00000013118	1 retrocopy	retro_shar_464,
Tursiops truncatus	ENSTTRG00000006988	1 retrocopy	retro_ttru_1394,