RetrogeneDB ID: retro_cjac_443

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:86689180..86690238(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAV1
• Ensembl ID: ENSCJAG00000006590
• Aliases: None
• Description: None

Sequence

>retro_cjac_443
GATCTTATGCCTTTATTCATCCGGCATGGTCCAACAATTCCCAGACGAACTGATATCTGTCTTCCAGATTCAAGCCCTAA
TGCCTTTTCAGCTTCTGGAGATGGGGTAGTTTGAAGAAACCAGAGTTTCCTTAGAACTCCAATTCAAAGAATACCTCATG
AAATAATGAGAAGAGAAAGCAACAGATTAGCTGCACCTTCTTATCTTGCCAGAAGTCTAGCAGATGTCCCTAGAGAGTAT
GGCTCTTCTCAGTCATTTGTAACGGAAGTTAATTTTGCTGTTGAAAATGGAGACTCTGGTTCCCGATATTATTATTCAGA
CAATTTTCTTGATGGTCAGAGAAAGCGGCCACTTGGAGATCGTACACATGAAGAATACAGATATTATGAATACAACCATG
ATTTCTTCCAAAGAATGCCTCAGAATCAGGGGAGGCATGCTTCAGGTATTGGGAGAGTTGCTACTACATCTTTAGGAAAT
TTGACTAACCAGGTTCTGAAGATTTACCCCTTCCTCCTGGCTGGTCTGTGGACTGGACAATGAAAGGGAGAAAATACTAT
ATAGATCATCACACAAATACAACTCACTGGAGCCAACCTCTTGAGCGAGAAGGCCTTCTTCCAGGATGGGAGCGAGTTGA
GTCATCAGAATTTGGAAACTATTATGTAGATCACACAAATAAGAAGGCTCAGTATAGGCATCCCTTTGCTCCTAGTGTAC
CTCAGTATGATCAGCCACCTCCTGTCACTTACCAGCCACAGCAAACTGAAAGAAATTAGTCCCTTCTGGTACCTGCAAAT
CCATATCATACTGCAGAAATTCCTGACTGGCTTCAGGTGTATGCTCGAGCCACTGTGAAATATGACCACATCCTGCAGTG
GGAACTCTTCCAGCTGGCTGACCTGGATACATACCAGGGAATGCTAAAGTCGCTCTTCATGAAAGAATTGGAGCAGATTG
TTAAGATGTATGAAGCATACAGACAAGCTCTTCTTACAGAGTTGGAAAACCGAAAGCAGAGACAGCAGTGGTTTGCCCAA
CAACATGAAAAAAATTTT

Alignment

ORF - retro_cjac_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 91.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLMPSFIRHGPTIPRRTDICLPDSSPNAFSASGDGVVSRNQSFLRTPIQRTPHEIMRRESNRLSAPSYLA
          .LMP.FIRHGPTIPRRTDICLPDSSPNAFSASGDGVV.RNQSFLRTPIQR.PHEIMRRESNRL.APSYLA
Retrocopy DLMPLFIRHGPTIPRRTDICLPDSSPNAFSASGDGVV*RNQSFLRTPIQRIPHEIMRRESNRLAAPSYLA

Parental  RSLADVPREYGSSQSFVTEVNFAVENGDSGSRYYYSDNFFDGQRKRPLGDRTHEEFRYYEYNHDLFQRMP
          RSLADVPREYGSSQSFVTEVNFAVENGDSGSRYYYSDNF.DGQRKRPLGDRTHEE.RYYEYNHD.FQRMP
Retrocopy RSLADVPREYGSSQSFVTEVNFAVENGDSGSRYYYSDNFLDGQRKRPLGDRTHEEYRYYEYNHDFFQRMP

Parental  QNQGRHASGIGRVAATSLGNLTNH-GSEDLPLPPGWSVDWTMRGRKYYIDHNTNTTHWSHPLEREGLPPG
          QNQGRHASGIGRVA.TSLGNLTN..GSEDLPLPPGWSVDWTM.GRKYYIDH.TNTTHWS.PLEREGL.PG
Retrocopy QNQGRHASGIGRVATTSLGNLTNQ<GSEDLPLPPGWSVDWTMKGRKYYIDHHTNTTHWSQPLEREGLLPG

Parental  WERVESSEFGTYYVDHTNKKAQYRHPRAPSVPRYDQPPPVTYQPQQTERNQSLLVPANPYHTAEIPDWLQ
          WERVESSEFG.YYVDHTNKKAQYRHP.APSVP.YDQPPPVTYQPQQTERN.SLLVPANPYHTAEIPDWLQ
Retrocopy WERVESSEFGNYYVDHTNKKAQYRHPFAPSVPQYDQPPPVTYQPQQTERN*SLLVPANPYHTAEIPDWLQ

Parental  VYARAPVKYDHILKWELFQLADLDTYQGMLKLLFMKELEQIVKMYEAYRQALLTELENRKQRQQWYAQQH
          VYARA.VKYDHIL.WELFQLADLDTYQGMLK.LFMKELEQIVKMYEAYRQALLTELENRKQRQQW.AQQH
Retrocopy VYARATVKYDHILQWELFQLADLDTYQGMLKSLFMKELEQIVKMYEAYRQALLTELENRKQRQQWFAQQH

Parental  GKNF
          .KNF
Retrocopy EKNF

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	7.59 RPM
SRP051959_heart	0.05 RPM	14.87 RPM
SRP051959_kidney	0.00 RPM	5.44 RPM
SRP051959_liver	0.04 RPM	5.74 RPM
SRP051959_lung	0.05 RPM	10.46 RPM
SRP051959_lymph_node	0.09 RPM	6.21 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.53 RPM
SRP051959_spleen	0.04 RPM	8.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_443 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_443 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006590	1 retrocopy	retro_cjac_443 ,
Dasypus novemcinctus	ENSDNOG00000005318	1 retrocopy	retro_dnov_125,