RetrogeneDB ID: retro_cjac_3042

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:885602..886304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSCJAG00000012622
• Aliases: None
• Description: STARD3 N-terminal like [Source:HGNC Symbol;Acc:19169]

Sequence

>retro_cjac_3042
ATGAGCCACCTGCCAGAAAACATGGAGAATGCTCTCACCGGAAGCCAGAGCTCCCACGCTTCTCTGCAAGACATTCATTC
CGTCAACCCCACACAACTCATGGCCAGGATTGAGCCCTATGAAGGAAGGGAAAAGAAAGGCATATCTCATGTCAGGAGGA
CTTTCTGTTTCTTTGTCACCTTTGACCTCTTATTTGTAACATGACTGTGGATAATAGAATTAAATGTGAATGGAGGCATT
GAGAATACGTTAGAGAAAGAGGAGGTGCAGTATGACTATTACTCTTCATATTTTGATATATTTCTTTTGGCAGTTTTTCA
ATTTAAAATATTAATACTTGCATACGCTGTGTGCAGACTGTGCCACTGGTGGGCAATAGCGTTGACAACGGCAGTGACCA
GTGCCTTTTTACTAGCAAAAGTGATCCTTTCAAAGCTTTTCTCTCAAGGGACTTTTGGCTATGTGCTCCCCATTATTTCA
TTCATCCTTGCCTGGATTGAGATGTGGTTCCTCGATTTCAAAGTGTTACCTCAAGAAGCAGCAGAAGAAAACAGGATCCT
GACAATTCAGGATGCTTCAGAGAGGGAAGCACTTATACCTGGCGGTCCTTCTGATGGTCAGTTTTATTCCCTTCCTGAAT
CTGAAGCAGGAACTGATGAAGCTGAAGAAAAACAGGACAGTGAGAAACCACTTTTAGAACTA

Alignment

ORF - retro_cjac_3042 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNHLPENMENALTGSQSSHASLRDIHSINPTQLMARIESYEGREKKGISDVRRTFCLFVTFDLLFVTLLW
          M.HLPENMENALTGSQSSHASL.DIHS.NPTQLMARIE.YEGREKKGIS.VRRTFC.FVTFDLLFVT.LW
Retrocopy MSHLPENMENALTGSQSSHASLQDIHSVNPTQLMARIEPYEGREKKGISHVRRTFCFFVTFDLLFVT*LW

Parental  IIELNVNGGIENTLEKEVVQYDYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWWAIALTTAVTSAFLLAK
          IIELNVNGGIENTLEKE.VQYDYYSSYFDIFLLAVF.FK.LILAYAVCRL.HWWAIALTTAVTSAFLLAK
Retrocopy IIELNVNGGIENTLEKEEVQYDYYSSYFDIFLLAVFQFKILILAYAVCRLCHWWAIALTTAVTSAFLLAK

Parental  VILSKLFSQGAFGYVLPIISFILAWIETWFLDFKVLPQEAEEENRLLIVQDASEREELIPGGLSDGQFYS
          VILSKLFSQG.FGYVLPIISFILAWIE.WFLDFKVLPQEA.EENR.L..QDASERE.LIPGG.SDGQFYS
Retrocopy VILSKLFSQGTFGYVLPIISFILAWIEMWFLDFKVLPQEAAEENRILTIQDASEREALIPGGPSDGQFYS

Parental  PPESEAGSDEAEEKQDSEKPLLEL
          .PESEAG.DEAEEKQDSEKPLLEL
Retrocopy LPESEAGTDEAEEKQDSEKPLLEL

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	0.31 RPM	9.58 RPM
SRP051959_heart	0.70 RPM	8.03 RPM
SRP051959_kidney	0.31 RPM	9.47 RPM
SRP051959_liver	0.19 RPM	3.70 RPM
SRP051959_lung	1.15 RPM	18.17 RPM
SRP051959_lymph_node	1.32 RPM	20.30 RPM
SRP051959_skeletal_muscle	0.96 RPM	4.06 RPM
SRP051959_spleen	0.99 RPM	15.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3042 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3042 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3042 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042 ,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,