RetrogeneDB ID: retro_cjac_3877

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285669.1:8121..9081(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016193
• Aliases: None
• Description: None

Sequence

>retro_cjac_3877
ACTGTTCTTGTTCAGTCCTGGGATCCAATCACAGTGGCCACAAATTCTAGAGAGCAGAAGAAAATATGGCCCAACTGTTT
GTTAGAAACTTCTGGTAACTGAGATGGTCTGGAATACAAGTTACATGATTTTGGCTACAGAGGAGTCTCTTGCCAAGAGA
CTGCTGGCATAGGAGCATCTGCTCATTTGGTTAACTTCAAAGGAACAGATACAGTAGCAGGAATTGCTCTTATAAAAAAA
TATTATGGAACGAAAGATCCTGTTCCAGGCTATTCTGTTCCAGCAGCAGAACACAGTACCATAACAGCCTGGGGGAAAGA
CCATGAAAAAGATGCTTTTGAACACACAGTAACACAGTTTTCATCAGTGCCTGTATCTCTGGTCAGCGATAGCTATGACA
TTTGTAATGTGTGTGAGAAAATATGGGGTGAAGATCTAAGACATTTAATAGTATCCAGAAGTACAGAGGCACCACTAATA
ATCAGACCTGATTCTGGAAACCCTCTCGACACTGTATTAAAGGTTTTGGAGATTTTAGGTAAGAAGTTTCCTGTTACTGA
GAACTCAAAGGGCTACAAGTCACTGCCACCTTATCTCACAGTGATTCAAGGGGATGGAGTAGATATTAATACCTTACAAG
AGATTGTAGAAGGCATGAAACTAAAAAAGTGGAGTATTGAAAATGTTTCCTTCGGTTCTGGTGGAGCTTTGCTACAGAGG
TTAACAAGAAATCTCTTGAATCGTTCCTTCAAGTGTAGTTATGTTGTAACCAATGGCCTTGGAATTGACGTCTTCAAGGA
CCCAGTTGCTGATCCCAACAAAAGGTCGAGAAAGGGCCGACTATCTTTACATAGGACACCAGCAGGGAATTTTGTTACAC
TGGAGGAAGGAAAAGGAGACCTTGAGGAATATGGTCATGATCTTCTCCATACTGTCTTCAAGAATGGCAAGGTGACAAAA

Alignment

ORF - retro_cjac_3877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.06 %
• Parental protein coverage: 65.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTD
          T.LVQSW.PITVATNSREQKKI....LLETSGN.DGLEYKLHDFGYRGVS.QETAGIGASAHLVNFKGTD
Retrocopy TVLVQSWDPITVATNSREQKKIWPNCLLETSGN*DGLEYKLHDFGYRGVSCQETAGIGASAHLVNFKGTD

Parental  TVAGIALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEK
          TVAGIALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEH.VTQFSSVPVS.VSDSYDI.N.CEK
Retrocopy TVAGIALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHTVTQFSSVPVSLVSDSYDICNVCEK

Parental  IWGEDLRHLIVSRSTEAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDIN
          IWGEDLRHLIVSRSTEAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYK.LPPYL.VIQGDGVDIN
Retrocopy IWGEDLRHLIVSRSTEAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKSLPPYLTVIQGDGVDIN

Parental  TLQEIVEGMKLKKWSIENVSFGSGGALLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGR
          TLQEIVEGMKLKKWSIENVSFGSGGALLQ.LTR.LLN.SFKCSYVVTNGLGI.VFKDPVADPNKRS.KGR
Retrocopy TLQEIVEGMKLKKWSIENVSFGSGGALLQRLTRNLLNRSFKCSYVVTNGLGIDVFKDPVADPNKRSRKGR

Parental  LSLHRTPAGNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTK
          LSLHRTPAGNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTK
Retrocopy LSLHRTPAGNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTK

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	0.07 RPM	44.06 RPM
SRP051959_heart	0.21 RPM	46.48 RPM
SRP051959_kidney	0.11 RPM	65.72 RPM
SRP051959_liver	0.11 RPM	234.78 RPM
SRP051959_lung	0.03 RPM	65.69 RPM
SRP051959_lymph_node	0.07 RPM	43.88 RPM
SRP051959_skeletal_muscle	0.07 RPM	108.16 RPM
SRP051959_spleen	0.23 RPM	72.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3877 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3877 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016193	2 retrocopies	retro_cjac_1281, retro_cjac_3877 ,
Cavia porcellus	ENSCPOG00000009226	1 retrocopy	retro_cpor_848,
Homo sapiens	ENSG00000105835	1 retrocopy	retro_hsap_79,
Oryctolagus cuniculus	ENSOCUG00000013417	1 retrocopy	retro_ocun_777,
Pongo abelii	ENSPPYG00000018270	2 retrocopies	retro_pabe_1407, retro_pabe_1415,
Pan troglodytes	ENSPTRG00000019571	1 retrocopy	retro_ptro_114,
Takifugu rubripes	ENSTRUG00000016695	1 retrocopy	retro_trub_33,