RetrogeneDB ID: retro_cjac_4133

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:139056095..139057319(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSCJAG00000006776
• Aliases: None
• Description: None

Sequence

>retro_cjac_4133
AGTGGCACCAGCATGATATCCTTGATTATTCCTCCCAAAGACCAGATTTCACGAGTGGCAAAATTGTTGGCAGATGAGTT
TGGAACTGCATCTAACATTAACTCATGAGTAAACCGCCTTTCAGTCCTGGGAGCCATTACATCTGTACAACAAAGACTCA
AACTTTATAACAAAGTACCTCCAAATGGTCTGGTTGTTTACTATGGAACAATTGTAACAGAAGAAGGAAAGGAAAAGAAA
GTCAACATTGACTTTGAACCTTTCGAACCAGTTAATACATCATTGTATTTGTGTGACAACAAATTCCATACAGACGCTCT
TATAGCACTACTTTCAGATGATAGCAAGTTTGGATTCATTGTAATAGATGGTAGTGGTGCACTTTTTGGCACACTCCAAG
GAAACACAAGAGAAGTCCTGCACAAATTCACTGTGGATCTCCCAAAGAAACATGGTAGAGGAGGTCACTTAGATTTGCGT
TTTGCCCGTTTAAGAATGGAAAAGCAACATAACTATGTTCGGAAAGTAGCAGAAACCGCTGTGCAGCTGTTTATTTCTGG
GGACAAAGTGAATGCGGCTGGTCTAGTTTTAGCTGGATCTGCTGACTTTAAAACTGAACTAAGTCAATCTGATATGTTTG
ATCAGAGGTTACAGCCAAAAGTTTTAAAATTAGTTGATATATCCTATGGTGGTGAAAATGGATTCAGCCAAGCTATTGAG
TTATCTACTGAAGTCCTCTCCAACGTGAAATTCATTCAAGAGAAGAAATTAATAGGATGATACTTTGATGAAATCAGCTA
GGACACGGGCAAATACTGTTTTGGCATTGAAGATACACTAAAGGCTTTGGAAATGGGAGCTGTAGAAATTCTAATAGTCT
ATGAAAATCTGGATATAATGAGATATGTTCTTCATTGCCAAGGCACAGAAGAGGAGAACATTCTCTATCTAACTCCAGAG
CAAGAAAAGGATAAATCTCATTTCACAGACAAAGAGACCAGACAGGAACATGAGCGTATTGAGAGCATGCCCCTGTTGGA
ATGGTTTGCTAACAACTATAAAAAATTTGGAGCTATGTTGGAAATTGTCACAGATAAATCACAAGAAGGGTCTCAGTTTG
TGAAAGGCTTTGGTGGAATTGGAGGTATCTGGGACGAGTAGAAAGATTTCCAGGGAATGGAATACCAAGGAGGAGACGAT
GAATTTTTTGACCTTGATGACTAC

Alignment

ORF - retro_cjac_4133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.14 %
• Parental protein coverage: 96.45 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGT
          .GTSMISLIIPPKDQISRVAK.LADEFGTASNI.S.VNRLSVLGAITSVQQRLKLYNKVPPNGLVVY.GT
Retrocopy SGTSMISLIIPPKDQISRVAKLLADEFGTASNINS*VNRLSVLGAITSVQQRLKLYNKVPPNGLVVYYGT

Parental  IVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGTLQGNTREVL
          IVTEEGKEKKVNIDFEPF.P.NTSLYLCDNKFHT.AL.ALLSDDSKFGFIVIDGSGALFGTLQGNTREVL
Retrocopy IVTEEGKEKKVNIDFEPFEPVNTSLYLCDNKFHTDALIALLSDDSKFGFIVIDGSGALFGTLQGNTREVL

Parental  HKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQS
          HKFTVDLPKKHGRGG...LRFARLRMEK.HNYVRKVAETAVQLFISGDKVN.AGLVLAGSADFKTELSQS
Retrocopy HKFTVDLPKKHGRGGHLDLRFARLRMEKQHNYVRKVAETAVQLFISGDKVNAAGLVLAGSADFKTELSQS

Parental  DMFDQRLQSKVLKLVDISYGGENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTL
          DMFDQRLQ.KVLKLVDISYGGENGF.QAIELSTEVLSNVKFIQEKKLIG.YFDEIS.DTGKYCFG.EDTL
Retrocopy DMFDQRLQPKVLKLVDISYGGENGFSQAIELSTEVLSNVKFIQEKKLIG*YFDEIS*DTGKYCFGIEDTL

Parental  KALEMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFA
          KALEMGAVEILIVYENLDIMRYVLHCQGTEEE.ILYLTPEQEKDKSHFTDKET.QEHE.IESMPLLEWFA
Retrocopy KALEMGAVEILIVYENLDIMRYVLHCQGTEEENILYLTPEQEKDKSHFTDKETRQEHERIESMPLLEWFA

Parental  NNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILRYRVDFQGMEYQGGDDEFFDLDDY
          NNYKKFGA.LEIVTDKSQEGSQFVKGFGGIGGI.....DFQGMEYQGGDDEFFDLDDY
Retrocopy NNYKKFGAMLEIVTDKSQEGSQFVKGFGGIGGIWDE*KDFQGMEYQGGDDEFFDLDDY

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	0.07 RPM	60.99 RPM
SRP051959_heart	0.05 RPM	47.31 RPM
SRP051959_kidney	0.11 RPM	74.10 RPM
SRP051959_liver	0.17 RPM	66.71 RPM
SRP051959_lung	0.02 RPM	58.03 RPM
SRP051959_lymph_node	0.09 RPM	42.42 RPM
SRP051959_skeletal_muscle	0.13 RPM	92.35 RPM
SRP051959_spleen	0.04 RPM	64.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4133 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133 ,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,