RetrogeneDB ID: retro_cjac_1185

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:11437450..11438628(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033919
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006580
• Aliases: None
• Description: None

Sequence

>retro_cjac_1185
GGATCCGGCGGAGGTGCCCGCGCTTCGCCTGCCACGCAGCCGCCACTGCTGCTGCAGCCTTCGGCCACCGGTCCCGACGC
GACAGTGGGCGGGCCAGCTCCGACCCCGCTGCTGCCCCGCTCAGCCACAGCCTCGGTCAAGATGGAGCCGGAGAACAAGT
ACCTGCCTGAACTCATGACGGAGGACTCACTCGACCCGTCCTTCACTCACGCCAGCAGCTGCTGACTGCAGAAATTGACA
AGATTCAGAAAGGAGACTCAAGAAAGGATGATGAGGAGAATTACTTGGATTTATTTTCTCACAAGAACATGAAACTGAAA
GAACGAGTGCTGATACCTGTCAAGCAGTATCCCAAGTTCAATTTTGTGGGGAAGATTCTTGGACCGCAAGGGAATACAAT
CAAAAGACTGCAGGAAGAGACTGGTGCAAAGATCTCTGTGCTGGGAAAGGGCTCAATGAGAGACAAAGTTAAGGAGGAAG
AGCTGCGCAAAGGTGGAGACCTCAAATATGCCCACTTGAATATGGATCTGCATGTCTTCATTGAAGTCTTTGGACCCCCA
TGTGAGGCTTACGCTCTTATGGCCCATGCCATGGAGGAAGTCAAGAAATTTCTGGTACCAGATATGATGGATGATATCTG
CCAGGAGCGATTTTTAGAGCCGTCCTACTTGAATGGAGTACCTGAACCCTCTCCTGGACGTGGGATGCCAGTGAGAGGCC
GGGGAGCTGCACCTCCTCCACCACCTATTCCCAGGGGCCGTGGTGTTGGACCACCTTATGGGGCTTTGGTACGTGGTACA
CCAGTGAGGGGAGCCATTACCAGAGGTACCACTGTGACTCGAGGCGTGCCACCCCCACCTACTGTGAGGGGTGCTCCAGC
ACCAAGAGCATGGACAGCGGGCATCCAGAGGATACCTTTGCCTCCACCTCCTGCACCAGAAACATATGAAGAATATGCAT
ATGATGATACATATGCAGAACAAAGTTACAAAGGCTATGAAGGCTCTTACAGCCAGAGTCAAGGGGACTCAGAATATTAT
GACTATGGACATGGGGAGGTTCAAGATTCTCATGAAGCTTATGGCCAGGACGACTGGAATGGGACCAGGCCATCACTGAA
GGCCCTTCCAGGTAGGCCCATGAAGGGAGCATACAGAGAGCACCCATATGGACATTAT

Alignment

ORF - retro_cjac_1185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.89 %
• Parental protein coverage: 94.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAHPSVRQTPSRQPPPLLPPSATGPDATVGGPAPTPLLPPSATASVKMEPENKYLPELMAEKDSLDPSFT
          G.....R..P..QPP.LL.PSATGPDATVGGPAPTPLLP.SATASVKMEPENKYLPELM.E.DSLDPSFT
Retrocopy GSGGGARASPATQPPLLLQPSATGPDATVGGPAPTPLLPRSATASVKMEPENKYLPELMTE-DSLDPSFT

Parental  HA-MQLLTAEIEKIQKGDSKKDDEENYLDLFSHKNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQ
          HA..QLLTAEI.KIQKGDS.KDDEENYLDLFSHKNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQ
Retrocopy HA<QQLLTAEIDKIQKGDSRKDDEENYLDLFSHKNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQ

Parental  EETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFIEVFGPPCEAYALMAHAMEEVKKFLVPD
          EETGAKISVLGKGSMRDK.KEEELRKGGD.KYAHLNMDLHVFIEVFGPPCEAYALMAHAMEEVKKFLVPD
Retrocopy EETGAKISVLGKGSMRDKVKEEELRKGGDLKYAHLNMDLHVFIEVFGPPCEAYALMAHAMEEVKKFLVPD

Parental  MMDDICQEQFLELSYLNGVPEPSRGRGVPVRGRGAAPPPPPVPRGRGVGPPRGALVRGTPVRGAITRGAT
          MMDDICQE.FLE.SYLNGVPEPS.GRG.PVRGRGAAPPPPP.PRGRGVGPP.GALVRGTPVRGAITRG.T
Retrocopy MMDDICQERFLEPSYLNGVPEPSPGRGMPVRGRGAAPPPPPIPRGRGVGPPYGALVRGTPVRGAITRGTT

Parental  VTRGVPPPPTVRGAPAPRARTAGIQRIPLPPPPAPETYEEYGYDDTYAEQSYEGYEGYYSQSQGDSEYYD
          VTRGVPPPPTVRGAPAPRA.TAGIQRIPLPPPPAPETYEEY.YDDTYAEQSY.GYEG.YSQSQGDSEYYD
Retrocopy VTRGVPPPPTVRGAPAPRAWTAGIQRIPLPPPPAPETYEEYAYDDTYAEQSYKGYEGSYSQSQGDSEYYD

Parental  YGHGEVQDSYEAYGQDDWNGTRPSLKAPPARPVKGAYREHPYGRY
          YGHGEVQDS.EAYGQDDWNGTRPSLKA.P.RP.KGAYREHPYG.Y
Retrocopy YGHGEVQDSHEAYGQDDWNGTRPSLKALPGRPMKGAYREHPYGHY

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	0.02 RPM	35.48 RPM
SRP051959_heart	0.02 RPM	36.75 RPM
SRP051959_kidney	0.02 RPM	39.36 RPM
SRP051959_liver	0.04 RPM	21.36 RPM
SRP051959_lung	0.07 RPM	41.14 RPM
SRP051959_lymph_node	0.00 RPM	42.10 RPM
SRP051959_skeletal_muscle	0.00 RPM	24.31 RPM
SRP051959_spleen	0.00 RPM	42.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1185 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1185 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1185 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006973	1 retrocopy	retro_chof_314,
Callithrix jacchus	ENSCJAG00000002780	1 retrocopy	retro_cjac_1930,
Callithrix jacchus	ENSCJAG00000006580	1 retrocopy	retro_cjac_1185 ,
Callithrix jacchus	ENSCJAG00000012368	1 retrocopy	retro_cjac_3262,
Dasypus novemcinctus	ENSDNOG00000003761	1 retrocopy	retro_dnov_2549,