RetrogeneDB ID: retro_cjac_4050

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:34811105..34812097(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002987
• Aliases: None
• Description: None

Sequence

>retro_cjac_4050
AAAATGTCCACAGAAGGTGGATTTTGTGGTACTAGCAGTAGTAATGCCCTGTAAAGCCTACAGTCCTTTCTGGCTTTGAG
TCCTGGAAGAAATCCAGAATTTAACAGTGAAAGATTTACTAGCACAGGAACTTCCATGGCCGGTATTAAGAAGATTTTGA
AACTGAATGATGTAAAGATGATCAGTAGAGAAGCTCCTGTGCTCTTTGTCAAGGCAGCCCAGATTTTTATCACAGAGTTG
ACTCTTTTAGCCTGGATTCACACAGAGGCTAAAAAGCACTGGACTCTATAGGGAAATGATGTCACCATAGGAATTACAAA
ATTAGATCAGTTTGACTTTCTCATTGATATTGTTTTAACAGATGAACGGAACCCTCCAAAGCATCAGGAAGAAGTGCGCC
AGTCTGTAATTACTGCCAAGCCCATCTAGAATTACTTCACACTGGCTTAGCAGCCTACCATGGGCCAAGTCTAGGGACAG
CAGCAAGGCCAGGAGACCACCAGCTCTATGACCACCATTCAGCTTGTGTAGATCATCATGTAGCCTCTGTGGGGACAGAT
CATGCCCCAGACAATGCAGGCTGGAGGTCAGCAGGTGCAGATTGTCCAGTCCCAACCACAGGGTCAAGCCTAACAGTCCC
AGAGTGACACTGGACAGACTATGCAGGTTATGTAACAGATTATTACTAAAACAGGAGAGATCCAATAGATCCCAGTGCAG
CTGAACTCAGGCCAGCTAGAATATATTTACTTAGTCCAGCCTGTATCAGGTATTCAAGTCATGCAGGAACAGGTCTAGAT
GCTTGCCACAATGCCCAACAGATTACACAAACAGAGGTCCAGTAAGGACAGCGGCAGTTCAACCAAGTCACAGATGTATA
CAAGCTCTACCAGATCGAGCAAGTCACCATTCCTGTGGACTAGGACCTTACCCAGCCCATGTTCAACAAGTCAGCAAACC
AGCTCTCCTATAGTCAGGATGCCTGGGTGACC

Alignment

ORF - retro_cjac_4050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.05 %
• Parental protein coverage: 97.95 %
• Number of stop codons detected: 14
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EMSAEGGFGGTSSSDAQQSLQSF-WPRVMEEIRNLTVKDFRVQELP-LARIKKIMKLDEDVKMISAEAPV
          .MS.EGGF.GTSSS.A..SLQSF.W..V.EEI.NLTVKD...QELP..A.IKKI.KL..DVKMIS.EAPV
Retrocopy KMSTEGGFCGTSSSNAL*SLQSF>WL*VLEEIQNLTVKDLLAQELP<MAGIKKILKLN-DVKMISREAPV

Parental  LFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVT
          LF.KAAQIFITELTL.AWIHTE..K..TL..ND....ITK.DQFDFLIDIV..DE..PPK.QEEVRQSV.
Retrocopy LFVKAAQIFITELTLLAWIHTEAKKHWTL*GNDVTIGITKLDQFDFLIDIVLTDERNPPKHQEEVRQSVI

Parental  PAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQVCELLRMPIQQDSVPVVGEK
          .A.P...YFTLA.QPT..QV.GQQQGQ.TTSS.TTIQ...II...P..GQ......M......V..V...
Retrocopy TAKPI*NYFTLA*QPTMGQV*GQQQGQETTSSMTTIQLV*IIM-*PLWGQIMP-QTMQAGGQQVQIVQSQ

Parental  LQGVVEEKKWGRGRLIDLFTEVYVNNYDYKELKVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLAT-NAQQ
          .QG.........G....................VQLN.GQL.YI.L.QPVSG.QV.Q.Q...LAT.NAQQ
Retrocopy PQGQA*QSQSDTGQTMQVM*QIITKTGEIQ*IPVQLNSGQLEYIYLVQPVSGIQVMQEQV*MLAT<NAQQ

Parental  ITQTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQAPQVT
          ITQTEVQ.GQ.QF.Q.TD...LYQI.QVT.P...DL.QPMF..SANQ.S..Q...VT
Retrocopy ITQTEVQ*GQRQFNQVTDVYKLYQIEQVTIPVD*DLTQPMFNKSANQLSYSQDAWVT

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	0.00 RPM	8.12 RPM
SRP051959_heart	0.00 RPM	13.66 RPM
SRP051959_kidney	0.02 RPM	18.19 RPM
SRP051959_liver	0.00 RPM	8.12 RPM
SRP051959_lung	0.00 RPM	12.10 RPM
SRP051959_lymph_node	0.00 RPM	13.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.82 RPM
SRP051959_spleen	0.00 RPM	13.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4050 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4050 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4050 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050 ,
Callithrix jacchus	ENSCJAG00000017156	1 retrocopy	retro_cjac_1087,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844,
Nomascus leucogenys	ENSNLEG00000012195	2 retrocopies	retro_nleu_2369, retro_nleu_2850,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,