RetrogeneDB ID: retro_cjac_1124

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:10077645..10078213(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM7
• Ensembl ID: ENSCJAG00000006678
• Aliases: None
• Description: None

Sequence

>retro_cjac_1124
ATTGATTCCTTCAAAGCATTGCTGGAGGGGTCAGCACCTTGAGGCTTCTGGCTGCAAGGGGCAAGGACCTCAATGTACCC
TTCTCCATTTCCTGGCTCACTCCTGGAGGCAAATCAGTGCAGGCTGGTGTGGCTGTGGGTGACTGGGTGCTCATCAAAGG
TGAGAAGGCAGGAAGTTCACATATATCAAAGCCCAGAACAAGATCTGAGCCTGCATAAAGCGCCTCAGCCTGGGTCTCAG
CAGGTCTCAGCCAGTTCAGAGCAAACCACAGGAAGTCCTGGCTCCTGCCACAACCCCCCTGCAGTTCATACTTGCACCCA
GCACTTTCCTCAACAAGATGGCCTGGCCCTTTAGGGCACCCCTACCCGCTGGCAGTGCACCACAGAATGGACAGCTGCTC
CAACTGCTGGTCCCAGATGCCACCAAGCAGTGGTTGATGGAGAATACCAAGACTGGACACCATGGCCTGGGACAGGCCAG
TCGTGTTCCTTCAGCAAACTTGCCCACCTCATAGACACTAGTTCATGCAGACCTGGATGAGGAGCACCTGAAGAAATCAA
GGGAAAAG

Alignment

ORF - retro_cjac_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.19 %
• Parental protein coverage: 86.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDSFKVVLEGPAPWGFRLQG-GKDFNMPLSISRLTPGGKAAQAGVAVGDWVLSIDGENAGS-LTHIEAQN
          .DSFK..LEG.AP.GF.LQG.GKD.N.P.SIS.LTPGGK..QAGVAVGDWVL.I.GE.AGS..T.I.AQN
Retrocopy IDSFKALLEGSAP*GFWLQG<GKDLNVPFSISWLTPGGKSVQAGVAVGDWVL-IKGEKAGS<FTYIKAQN

Parental  KIRACGERLSLGLSRAQPVQSKPQKAPAPAADPPRYTFAPSVSLNKTARPFGAPPPADNAPQQNGQPLRP
          KI.AC..RLSLGLSR.QPVQSKPQ...APA..P.....APS..LNK.A.PF.AP.PA..AP.QNGQ.L..
Retrocopy KI*ACIKRLSLGLSRSQPVQSKPQEVLAPATTPLQFILAPSTFLNKMAWPFRAPLPAGSAP-QNGQLLQL

Parental  LVPDASKQRLMENT-EDWRPRPGTGQSRSFRILAHLTGTE-FMQ-DPDEEHLKKSREK
          LVPDA.KQ.LMENT..DW.P.PGTGQS.SF..LAHL..T..FMQ.D.DEEHLKKSREK
Retrocopy LVPDATKQWLMENT<QDWTPWPGTGQSCSFSKLAHLIDTS<FMQ<DLDEEHLKKSREK

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	5.90 RPM
SRP051959_heart	0.46 RPM	17.86 RPM
SRP051959_kidney	0.09 RPM	2.48 RPM
SRP051959_liver	0.11 RPM	0.89 RPM
SRP051959_lung	0.05 RPM	4.78 RPM
SRP051959_lymph_node	0.07 RPM	3.70 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.09 RPM
SRP051959_spleen	0.00 RPM	3.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1124 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1124 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	ENSCJAG00000006678	1 retrocopy	retro_cjac_1124 ,
Homo sapiens	ENSG00000196923	1 retrocopy	retro_hsap_3940,
Macaca mulatta	ENSMMUG00000003146	1 retrocopy	retro_mmul_2283,