RetrogeneDB ID: retro_cjac_1045

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:73975367..73976807(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHQ1
• Ensembl ID: ENSCJAG00000015131
• Aliases: None
• Description: None

Sequence

>retro_cjac_1045
GCTCTTCTGGCACCAAGAAAATCCAGGACAGCAAGACCACTTTTGGAAGAAATAGGTGCTTCTGAGATTCCTGAAGAAGT
AGTTGATGATGAAGAGTTTGATTGGGAAATTGAGCAGACATCCTATGAATAGGTATCAGAAAGTGCTATGAATCCGCAGT
GCCACTGTGGATTTGGAAACTTACAATCAGGAGTGTTTCAGTGGTTACAGGATGAATTGAGTGATGTTATTGATATTAAG
GATCTAGATTTCAGCCCTGCAGCTGAACCAAGACAGAAGTGCCTGGCCACTGAGCTGGCCGAGTTTGATCCTGATCATTA
TCTAACTGACATTTTTGAAGATGAGGCGGTTGAACAGATTTTGAAGTACAATCCATGGTGGACTGACAAATATTAAAAAA
TGACAGCCTTTTTGGAAAAGAGTCAGGAGCAAGAAATCATGCTTCTTTAGTGTCTTTTTCTGAAGAAGAAAAATATCAGC
TACAAAAATTTGTCAATAAATCTTATCTGTTGGACAAGAGAACCTGTTGTCAAGTGTACTACAGTTTGATTGATGTCCTT
CTGGAATATTGCTATGAAACCTGTGTCACTGAAGGAGAGAAGAATGTTGAATCTGCATGGAATATCAGGAAACTGAGTCC
AACATTATGGTGGTTTGAGACTTGGACTAATGTTCATGCTATCATGGTGTCTTTTGGAAGAAGGGTGTTGTGTTACCCAC
TCCACTGCCATTTCAAGCTGGTGATGAAGGCCTAGAGGAACACTATATAGATATTACAACTAGGTAAAAGTGCAGTTTTA
AAGTATCTCTGGATATTCACAAAATTTTTCAGGAAAACAACACAGCATAAATACTGAATGATCTCTACATCTCAGACTAC
TGTGTGAATTCAGAAAGTCAAATCTAAAAGTTGGCAGTTCTTGCAGAAGAAGCCTTAAAGGAAATCTCCCTTACAAAGGC
CCAGCTGGGGTTAGAACTGGAAGAACTAGCAGCAGCAGCACTTCTTGTCCAGGAAGAAACTGCATTAAAAGCAGCCCATT
CAGTATCTAGGCAGCAGACACTTTGCTCCAGATCTGAGGCAAGTGATATAGAGGAGTCAGACAGCACCGTGTCATCTGGA
AATGAAGACTCAGACTCAGATTCAAAACAAGTTAAACTCAAAGATAGTCCATCTAAGACAGTCAGTTCTTTGCAAGGTCC
CTTTGTGGAAAGCAGTGCCCTTCTTATTGTTGATGGTGGAGTATGCAGAAACATAGCCATCCAGGAATCCGATGCCAGTC
AAGGAAAGTCACTTGCCTCTTCCCAGTGTTTTGGAGTGCCTGGGCCTCTGATAGCGGAGTGTGGGGAACAAATGAAGACC
ACAGTTCAAGTTTCTGAACCCAAGGGCACCACTGCTGTAACAATATGCAGGAGAGAGACAGCTGTCAGACACCAAATAAT

Alignment

ORF - retro_cjac_1045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 84.03 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ALLAPRKSRTAKPLVEELGASEIPEEVVDDEDFDWEIEQTPYEEVSESALNPQCHYGFGNLRSGVFQRLQ
          ALLAPRKSRTA.PL.EE.GASEIPEEVVDDE.FDWEIEQT.YE.VSESA.NPQCH.GFGNL.SGVFQ.LQ
Retrocopy ALLAPRKSRTARPLLEEIGASEIPEEVVDDEEFDWEIEQTSYE*VSESAMNPQCHCGFGNLQSGVFQWLQ

Parental  DELSDVVDIKDPDFTPAVERRQKRLAAELAKFDPDHYLADFFEDEAVEQILQYNPWWTDIYSKMTAFVEK
          DELSDV.DIKD.DF.PA.E.RQK.LA.ELA.FDPDHYL.D.FEDEAVEQIL.YNPWWTD.Y.KMTAF.EK
Retrocopy DELSDVIDIKDLDFSPAAEPRQKCLATELAEFDPDHYLTDIFEDEAVEQILKYNPWWTDKY*KMTAFLEK

Parental  SQEKE-NRAALVSFSEEEKYQLRKFLNKSYLLDKRACRQVCYSLIDILLAYCYETRVTEGEKNVESAWNI
          SQE.E.N.A.LVSFSEEEKYQL.KF.NKSYLLDKR.C.QV.YSLID.LL.YCYET.VTEGEKNVESAWNI
Retrocopy SQEQE<NHASLVSFSEEEKYQLQKFVNKSYLLDKRTCCQVYYSLIDVLLEYCYETCVTEGEKNVESAWNI

Parental  RKLSPTLCWFETWTNVHDILVSFGRRVLCYPLFRHFKLVMKAYRDTIKILQLGKSAVLKCL-LDIHKIFQ
          RKLSPTL.WFETWTNVH.I.VSFGRRVLCYPL..HFKLVMKA.R.TI.ILQLGKSAVLK.L.LDIHKIFQ
Retrocopy RKLSPTLWWFETWTNVHAIMVSFGRRVLCYPLHCHFKLVMKA*RNTI*ILQLGKSAVLKYL<LDIHKIFQ

Parental  ENDPAYILNDLYISDYCVWIQKVKSKKLAALAEALKEVSLTKAQLGLELEELEAAALLVQEEETALKAAH
          EN..A.ILNDLYISDYCV.......K......EALKE.SLTKAQLGLELEEL.AAALLVQ.EETALKAAH
Retrocopy ENNTA*ILNDLYISDYCVNSESQI*KLAVLAEEALKEISLTKAQLGLELEELAAAALLVQ-EETALKAAH

Parental  SVSGQQILSSSSEASDSEDSDSTVSSGNEDSDSDSEQDEPKDSPSETVSSLQGSFLEESSALLIVDGGVC
          SVS.QQ.L.S.SEASD.E.SDSTVSSGNEDSDSDS.Q...KDSPS.TVSSLQG.F..ESSALLIVDGGVC
Retrocopy SVSRQQTLCSRSEASDIEESDSTVSSGNEDSDSDSKQVKLKDSPSKTVSSLQGPFV-ESSALLIVDGGVC

Parental  RNTAIQEFDVSQGKPLASSRPLGPSGPLIEELGEQLKTTVQVSEPKGTTAV-NHSMQERDSCQTPNN
          RN.AIQE.D.SQGK.LASS...G..GPLI.E.GEQ.KTTVQVSEPKGTTAV.N.....RDSCQTPNN
Retrocopy RNIAIQESDASQGKSLASSQCFGVPGPLIAECGEQMKTTVQVSEPKGTTAV<NNMQE-RDSCQTPNN

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	0.42 RPM	11.71 RPM
SRP051959_heart	0.88 RPM	5.65 RPM
SRP051959_kidney	0.62 RPM	9.41 RPM
SRP051959_liver	0.35 RPM	8.01 RPM
SRP051959_lung	0.94 RPM	10.17 RPM
SRP051959_lymph_node	0.43 RPM	17.76 RPM
SRP051959_skeletal_muscle	0.46 RPM	6.35 RPM
SRP051959_spleen	0.32 RPM	14.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1045 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015131	1 retrocopy	retro_cjac_1045 ,
Homo sapiens	ENSG00000144736	1 retrocopy	retro_hsap_674,
Gorilla gorilla	ENSGGOG00000034818	1 retrocopy	retro_ggor_581,
Nomascus leucogenys	ENSNLEG00000002731	1 retrocopy	retro_nleu_463,
Pongo abelii	ENSPPYG00000013717	1 retrocopy	retro_pabe_546,
Pan troglodytes	ENSPTRG00000015106	1 retrocopy	retro_ptro_486,