RetrogeneDB ID: retro_cjac_1459

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:28345225..28346364(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033737
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020641
• Aliases: None
• Description: None

Sequence

>retro_cjac_1459
ATGATTTCTTCAACGTCCAGATTTGGCATACACTATGGCCTCAAGACTCTACTTGAAGGAATTAGCAGAGCCACTATCAA
AAGCAACCCATCAAACATCAACCAGTTTGTAGTAGTTTATTTTGAAGAACTTACTATGTATAGAGAAGGGAATAGTTCTC
TGGATATAAAGGATCTGGTTAAACAGCTTCATCAGATTAAAGTACAGAAGTGGTCAGAGGATCAATATGAACGAAGAAAG
TAGAATGTTTAAAAGAACCAGGAAAAAAAAAATCTGTAGAATCTAAAGTACCTACACGGATGGAAAAATCTACAGACAGA
GGAGAACAATGTAACCGGAACAGGATATAGTGACAAAACCACCCAGTTTCCATCAACTTATGCTGAGCTAGGCGCTGAGC
AAACTGAAGCAGTTCATGATTCTCCTCCCAAAGCAGCTACCCCTAAGACTACTACCCTACCCTCCTCACCACCTCCAACA
GCTGTCTCACCAGAGTTTGCCTATAGCCCAGCTGACCCAGCTCAGTTTGCTGCTCGGATGTTAGCAATGGCAGCAAGCGA
ATCAGAACAGCCACCACCATATTCCAACCTGTGGACCCTTTATTGTCTAACTGATAAGAATCAACAAAGTCACTCACCAC
TCCCACCTGCACCTGGGCCTTTCCCCCGAGCAACCCTCTACATATCTAATCTTAAGGATCCGCAATTTCTGCAGCATCCA
CCAACAGTCACTCCTCCAATTTATGTGATCGACGACACAAAGATCAGTGCCCCATCTTTTATCTCAGTTGCCTCAAATGT
TCAGAAAGCACAGGAATGGGAACCTCTTCCGGGACATGCTGTTGTTTCGCAGTCAGATGTCCTGAAGAGATACGCTGCAG
TGCAAGTGCCTGTTGCTGTTCCTGCAGATGGGAAATTCCAGAAACATACTCTAAGTCCCCACAATGCTAATCCTCCAAGT
GGACAAGATGTCTCCAATCCAAAAAGCCCTGTTTTTCATTCTGTTGCTTTCCCAGTAGAAGATGTAGCTAAAAAAGTTCA
AGATCTGGTGACAAATGGGCTCCCTTTGGAAGTTACGGTATTGCTGGGGAGATAAGTGTGGCTACCGCTCACAAAGTTCG
CAAAGCAGAAACCGAAAAC

Alignment

ORF - retro_cjac_1459 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MISSKPRFCIPYGLKTLLEGISIAIIKSNPSNIVQFAAVYFEELTMYRV-NTSLDIKDLVKQFHQIKVQK
          MISS..RF.I.YGLKTLLEGIS.A.IKSNPSNI.QF..VYFEELTMYR..N.SLDIKDLVKQ.HQIKVQK
Retrocopy MISSTSRFGIHYGLKTLLEGISRATIKSNPSNINQFVVVYFEELTMYREGNSSLDIKDLVKQLHQIKVQK

Parental  WSE-GSIRPKKAECLKEP-EKSSVESKVPTHMEKSTDTEEDNVTGTGYSDKTTQFPSTYAELGAEQTEAV
          WSE.GSI..KK.ECLKEP.EK.........H..K...TEE.NVTGTGYSDKTTQFPSTYAELGAEQTEAV
Retrocopy WSE<GSI*TKKVECLKEP>EKKNL*NLKYLHGWKNLQTEENNVTGTGYSDKTTQFPSTYAELGAEQTEAV

Parental  HDSSPKAATPKTTTPPFSPPPTAVSPEFAYVPADPAQFAAQMLAMAASEPEQLPPYSNMWTLYCLTD-NQ
          HDS.PKAATPKTTT.P.SPPPTAVSPEFAY.PADPAQFAA.MLAMAASE.EQ.PPYSN.WTLYCLTD.NQ
Retrocopy HDSPPKAATPKTTTLPSSPPPTAVSPEFAYSPADPAQFAARMLAMAASESEQPPPYSNLWTLYCLTDKNQ

Parental  QSHSSPPPAPGPFPQATLYISNPKDPQFLQHPPTVTSPIYVMDDTKKISAPPFILVGSKFQKAQEWEPLP
          QSHS..PPAPGPFP.ATLYISN.KDPQFLQHPPTVT.PIYV.DDT.KISAP.FI.V.S..QKAQEWEPLP
Retrocopy QSHSPLPPAPGPFPRATLYISNLKDPQFLQHPPTVTPPIYVIDDT-KISAPSFISVASNVQKAQEWEPLP

Parental  GHAVVSQSDVLKRYAAVQVPIAVPADGKFQKHTLSPHNANPPSGQDVPKPKSPVFLSVAFPVEDVAK-NN
          GHAVVSQSDVLKRYAAVQVP.AVPADGKFQKHTLSPHNANPPSGQDV..PKSPVF.SVAFPVEDVAK...
Retrocopy GHAVVSQSDVLKRYAAVQVPVAVPADGKFQKHTLSPHNANPPSGQDVSNPKSPVFHSVAFPVEDVAK<KS

Parental  SGSGDKCAPFGSYGIAGEITVATAHKVRKAETEN
          S.SGDK.APFGSYGIAGEI.VATAHKVRKAETEN
Retrocopy SRSGDKWAPFGSYGIAGEISVATAHKVRKAETEN

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	3.02 RPM
SRP051959_heart	0.00 RPM	5.24 RPM
SRP051959_kidney	0.00 RPM	5.52 RPM
SRP051959_liver	0.00 RPM	2.14 RPM
SRP051959_lung	0.00 RPM	5.53 RPM
SRP051959_lymph_node	0.00 RPM	5.34 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.76 RPM
SRP051959_spleen	0.00 RPM	6.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1459 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1459 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1459 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020641	1 retrocopy	retro_cjac_1459 ,
Cavia porcellus	ENSCPOG00000008281	1 retrocopy	retro_cpor_1541,
Loxodonta africana	ENSLAFG00000014928	1 retrocopy	retro_lafr_899,