RetrogeneDB ID: retro_cjac_2151

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:77169976..77170916(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSCJAG00000006231
• Aliases: None
• Description: None

Sequence

>retro_cjac_2151
AGTCTCATCAGCTGGGTGAAGAATGCCAAGAAAGAATGGAAAGAATCCTTGCCTAACCTGCTATAGTATGTAGTATGGAT
GCCCCTGCTAATCCTCAGGTATTTCATGGATGTAATAGATGCTGATCTTTTCATCCACTGTAGTTTACAATGCAGGGTTC
TGGCTGATGAAGCAAGAAAGTTTCATCTGAGGCCTGAACTTCAGAGTCAAATGCAGGGACCCAGGACAAGGGCTGGCCTA
GGTGCCAATGAAGTGCTTTTAGTAGTTGGGGTTTCAGAAGCCAGCAGTTTCCCATCAACATGGTAGAGAAATGTGATCTC
AAGAGTCAGGAGTGGATCTTTTTGCCAAACATCACTTGTAAGAGACGTTATGTGGCCTCGGTGTCCCTGTATGACTGAAT
CTACGTCATTGGTGGCTATGACAGCCATTCCCATCTTAGTTCAGTGGAATGTCTAGATTACACAGCAGATGAGGATGGGG
TCTGGTATTCTGTGGCCCCTATGAATTTCCAACAAGGTTGTTCCGGAGCCACCACTCTGGGAGATATGATCTATGTCTCT
GGAGGCTTCGATGGAAGCAGGTGTCACACCATTATGGAGCTGTATGATCCAAACATTGACCAGTGGACTATGCTGGCAGA
TGTCAGACAGTCTGGGAAGGTGTCCGACTCGTAGTGGCCTGCAGAGTGATCTACTGTCTAGGAGGATATAATGGCTTGAA
TATCTTAAATTCAACTGAGAAACATGACCCTTGTACAGGACATAGGACTACTGTTACAACAATGGCCACCAAGCATTCTA
GTGCAGGGGTAGCCTTGCTGAATGACCATATTTATGCAGTGAGGAGATTTGATGGTACAACGCACCTTTCTTCCACCGAA
GCATAAAACATTCGCACTGATTGCTGGAATGAAGAGTATGACCACTCCACCATGGTATGT

Alignment

ORF - retro_cjac_2151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVINWVKHAKKEREESLPNLLQYVR-MPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRSQ
          ..I.WVK.AKKE..ESLPNLL.YV..MPLL..RY..DVIDA..FI.CSLQCR.L.DEA.KFHLRPEL.SQ
Retrocopy SLISWVKNAKKEWKESLPNLL*YVVWMPLLILRYFMDVIDADLFIHCSLQCRVLADEARKFHLRPELQSQ

Parental  MQGPRTRARLGANEVLLVVG-GFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGG
          MQGPRTRA.LGANEVLLVVG.GF.SQQ.PI..VEK.D.K.QEW.FLP.IT.KRRYVASVSL.D.IYVIGG
Retrocopy MQGPRTRAGLGANEVLLVVG<GFRSQQFPINMVEKCDLKSQEWIFLPNITCKRRYVASVSLYD*IYVIGG

Parental  YDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQW
          YD..S.LSSVECLDYTADEDGVWYSVAPMN...G..GATTLGDMIYVSGGFDGSR.HT.ME.YDPNIDQW
Retrocopy YDSHSHLSSVECLDYTADEDGVWYSVAPMNFQQGCSGATTLGDMIYVSGGFDGSRCHTIMELYDPNIDQW

Parental  SMLGDM-QTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTTVTPMATKRSGAGVALLNDHI
          .ML.D..QT..EG..LVVA..VIYCLGGY.GLNILNS.EK.DP.TGH.TTVT.MATK.S.AGVALLNDHI
Retrocopy TMLADV<QTVWEGVRLVVACRVIYCLGGYNGLNILNSTEKHDPCTGHRTTVTTMATKHSSAGVALLNDHI

Parental  YVVGGIDGTAHLSSVEAYNIRTDSWTTVTSMTTPRC
          Y.V...DGT.HLSS.EA.NIRTD.W.......T..C
Retrocopy YAVRRFDGTTHLSSTEA*NIRTDCWNEEYDHSTMVC

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	17.24 RPM
SRP051959_heart	0.00 RPM	18.82 RPM
SRP051959_kidney	0.00 RPM	27.51 RPM
SRP051959_liver	0.00 RPM	18.61 RPM
SRP051959_lung	0.00 RPM	24.43 RPM
SRP051959_lymph_node	0.00 RPM	21.35 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.15 RPM
SRP051959_spleen	0.00 RPM	28.30 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2151 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2151 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151 ,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103, retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,