RetrogeneDB ID: retro_cjac_1187

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:14715579..14716696(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000015282
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPRA1
• Ensembl ID: ENSCJAG00000008960
• Aliases: None
• Description: transmembrane protein, adipocyte asscociated 1 [Source:HGNC Symbol;Acc:30413]

Sequence

>retro_cjac_1187
ATGGACACCCTGGAGGAGGCAACTTAGGCCAATGGGAGCACAGCACTGCTCCCACCCCTGGCGCCAAACATCAGTGTACC
TCATCGCTGCCTGCTGCTGCTCTACGAAGACATTGGCACCTCTAGGGTCCAGTACTGGGACCTCATGCTGCTCATCCCCA
ATGTGCTCTTCCTCATCTTCCTGCTCGCGAAGCTTCCATCTGTTCGGGCCAAGATCCGCATGACCTCCAGCCCCATTTTT
ATTACCTTCTACATCCTGGTGTTCGTGGTGGCGCTGGTAGGCGTTGGCTGGGCCGTGGTGTCCATGACGGTGAGCACCTC
GGATGCTTCAACTGTTGCTGATAAGATGCTGTGGGAGATCACCTGCTTCCTCCTGCTGGCATCGAGCTGAGTGTGATCAT
CCTGGGTCTGGCCTTCGGCCACCTGGAGAACAAGTACAGCATCAAGCAGGTGCTGGCCATCACCATGGTGTTGTCCCTGG
CCTATTCTGTCACCCAGGGGACCCTGGAGACCCTGTACCCTGATGCCCATCTCTCAGCTGAGGACTTTAACATCTATGGC
CATGGGGGCCGCCAGTTCTGGCCGGTCAGCTCCTGCTGCTTCTTCCTGGTATACTCTGGTGGTCATCCTCCCCAAGACCC
GGCTGAAGGAGTGCATTTTCCTGCCTTCTCGGAGGAGCTTCTACGTGTATGCGGGCATCCCGGCGCTGCTCAACCTGCTA
CAGGGGCTGGGGAGTGTGCTGCTGTGCTTGGACATCATCGAGGGGCTCTGCTGTGTAGACACCACAACCTTCCTATACTT
CAGTTTTTTTCGTGCTGCTCATCTATGTGGCCTTCCTCCGGAGCTTCTTCCTCTCGGAACCCAAGATCCTCTTCTCCTAC
AAATGCCAAGTGGATGAGACAGAGGAGCCAGACATACAGCTACCCCAGCCCTACGCTGTGGCCCAGCAGGAGGGCCTGGA
GGCTGCAGGGGCTGCTGGGGCCTCAGCTGCCAGTTACTCGAGCACGCAGTTCGACTCTGCTGGTGGGGTGGCCTACCTGG
ACGACATCGCTTCCATGCCCTGCCGTACTGGCAGCATCAACAGCACGGACAGTGAGCGTTGGGAGGCCATCAATGCC

Alignment

ORF - retro_cjac_1187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDTLEEATGANGSTALPPPLAPNISVPHRCLLLLYEDIGTSRVRYWDLMLLLPNVLFLIFLLWKLPSARA
          MDTLEEAT.ANGSTAL.PPLAPNISVPHRCLLLLYEDIGTSRV.YWDLMLL.PNVLFLIFLL.KLPS.RA
Retrocopy MDTLEEAT*ANGSTALLPPLAPNISVPHRCLLLLYEDIGTSRVQYWDLMLLIPNVLFLIFLLAKLPSVRA

Parental  KIRITSSPIFITFYILVFVVALVGIARAVVSMTVSTSDAATVADKILWEITRFFLLA-IELSVIILGLAF
          KIR.TSSPIFITFYILVFVVALVG...AVVSMTVSTSDA.TVADK.LWEIT.F.LLA.IELSVIILGLAF
Retrocopy KIRMTSSPIFITFYILVFVVALVGVGWAVVSMTVSTSDASTVADKMLWEITCFLLLA<IELSVIILGLAF

Parental  GHLESKSSIKRVLAITTVLSLAYSVTQGTLEILYPDAHLSAEDFNIYGHGGRQFWLVSSCFFFLVYS-LV
          GHLE.K.SIK.VLAIT.VLSLAYSVTQGTLE.LYPDAHLSAEDFNIYGHGGRQFW.VSSC.FFLVYS..V
Retrocopy GHLENKYSIKQVLAITMVLSLAYSVTQGTLETLYPDAHLSAEDFNIYGHGGRQFWPVSSCCFFLVYS>VV

Parental  VILPKTPLKERISLPSRRSFYVYAGILALLNLLQGLGSVLLCLDIIEGLCCVDTTTFLYFSFFAP-LIYV
          ..LPKT.LKE.I.LPSRRSFYVYAGI.ALLNLLQGLGSVLLCLDIIEGLCCVDTTTFLYFSFF...LIYV
Retrocopy I-LPKTRLKECIFLPSRRSFYVYAGIPALLNLLQGLGSVLLCLDIIEGLCCVDTTTFLYFSFFRA>LIYV

Parental  AFLRGFFGSEPKILFSYKCQVDETEEPDVHLPQPYAVARREGLEAAGAAGTSAASYSSTQFDSAGGVAYL
          AFLR.FF.SEPKILFSYKCQVDETEEPD..LPQPYAVA..EGLEAAGAAG.SAASYSSTQFDSAGGVAYL
Retrocopy AFLRSFFLSEPKILFSYKCQVDETEEPDIQLPQPYAVAQQEGLEAAGAAGASAASYSSTQFDSAGGVAYL

Parental  DDIASMPCHTGSINSTDSERWKAISA
          DDIASMPC.TGSINSTDSERW.AI.A
Retrocopy DDIASMPCRTGSINSTDSERWEAINA

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	6.50 RPM
SRP051959_heart	0.05 RPM	9.10 RPM
SRP051959_kidney	0.02 RPM	10.76 RPM
SRP051959_liver	0.00 RPM	12.76 RPM
SRP051959_lung	0.05 RPM	11.14 RPM
SRP051959_lymph_node	0.05 RPM	11.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.28 RPM
SRP051959_spleen	0.04 RPM	11.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1187 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1187 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008960	1 retrocopy	retro_cjac_1187 ,