RetrogeneDB ID: retro_cjac_2430

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:34763412..34764513(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022183
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LRRC28
• Ensembl ID: ENSCJAG00000016965
• Aliases: None
• Description: None

Sequence

>retro_cjac_2430
ATGGCATCTGAACTTTGTAAGACGATCTCTGTGGCAAGGCTGGAAAAGCACAAGAATTTGTTCTTAAATTACAGGAATCT
GCACCATTTTCCTTTGGAGTTACTAAAAGAAGAGGGACTGCAGTACTTGGAGAGACTCTATATGAAAAGGAACTCCCTGA
CAACCTTGCCAGAAAACCTTGCTCAGAAGCTTCCAAACCTTGTGGAACTATACCTGCACTCAAATAACATAGTTGTGGTA
CCAGAAGCCATTGGGTCCCTTGTAAAACTCCAATGTCTGGATCTTAGTGACAATGCCTTAGAAATAGTTTGCCCAGAAAT
TGGTCGTCTGCAAGCTTTACATCATCTTCAATTAGCTAATAACCAGCTGCAATTCCTACCTCCAGAGGTTGGCGATTTGA
AGGAGCTGCAGACACTAGACATTTCTACCAATTGTTTGCTAACTTTACCCGAGAGGCTTCACATGTGCCTTTCTCTGCTG
TACCTCACAGTGGACCGAAATCGTCTATGGTATGTGCCGCGCCATCTCTGCCAGCTGCCCAGCCTCAATGAGCTCTCCAT
GGCTGGAAACCGTCTTGCATTTTTGCCACTTGATTTAGGTCGATCTCGAGAACTACAATATGTGTACATGGATAACAACA
TAAACCTGAAAGGCTTGCCATCTTATCTGTACAATAAAGTCATCGGCTGCAGTGGCTGTGGTGCTCCCATTCAAGTTTCC
GAGGTGAAGCTGCTTTCCTTTTCATCAGGGCCTCAAACCGTTTTCCTCCCAGCCGAGGTAAAGGCCATAGGGACAGAGCA
TGATCACATCCTCCCTCTGCAGGAATTGGCCATGAGAAGTCTGTATCATACCTACCACAGCTTTCTGAAAGATTTGAACT
TTCTGTCTCCAATCTCATTACCCAGAAGTCTCCTAGAGCTGCTGCACTGCCCTCTGGGGCACTGTCTTCGGTGTAGTGAG
CCTATGTTTACCATCGTCTACCCCAAGCTCTTTCCCTTGAGAGAGACGCCAATGGCAGGGCTGCACCAGGGGAGAACAAC
TGTTAGTTTTGTGGCTTACTGCTGCTCCACCCAGTGTCTGCAGACTTTTGACCTGCTGAGT

Alignment

ORF - retro_cjac_2430 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASELCKTISVARLEKHKNLFLNYRNLHHFPLELLKDEGLQYLERLYMKRNSLTTLPENLAQKLPNLVEL
          MASELCKTISVARLEKHKNLFLNYRNLHHFPLELLK.EGLQYLERLYMKRNSLTTLPENLAQKLPNLVEL
Retrocopy MASELCKTISVARLEKHKNLFLNYRNLHHFPLELLKEEGLQYLERLYMKRNSLTTLPENLAQKLPNLVEL

Parental  YLHSNNIVVVPEAIGSLVKLQCLDLSDNALEIVCPEIGRLRALRHLRLANNQLQFLPPEVGDLKELQTLD
          YLHSNNIVVVPEAIGSLVKLQCLDLSDNALEIVCPEIGRL.AL.HL.LANNQLQFLPPEVGDLKELQTLD
Retrocopy YLHSNNIVVVPEAIGSLVKLQCLDLSDNALEIVCPEIGRLQALHHLQLANNQLQFLPPEVGDLKELQTLD

Parental  ISTNRLLTLPERLHMCLSLQYLTVDRNRLWYVPRHLCQLPSLNELSMAGNRLAFLPLDLGRSRELQYVYV
          ISTN.LLTLPERLHMCLSL.YLTVDRNRLWYVPRHLCQLPSLNELSMAGNRLAFLPLDLGRSRELQYVY.
Retrocopy ISTNCLLTLPERLHMCLSLLYLTVDRNRLWYVPRHLCQLPSLNELSMAGNRLAFLPLDLGRSRELQYVYM

Parental  DNNINLKGLPSYLYNKVIGCSGCGAPIQVSEVKLLSFSSGPRTVFLPAEVKAIGTEHDHILPLQELAMRS
          DNNINLKGLPSYLYNKVIGCSGCGAPIQVSEVKLLSFSSGP.TVFLPAEVKAIGTEHDHILPLQELAMRS
Retrocopy DNNINLKGLPSYLYNKVIGCSGCGAPIQVSEVKLLSFSSGPQTVFLPAEVKAIGTEHDHILPLQELAMRS

Parental  LYHTYHRFLKDLNFLSPISLPRSLLELLHCPLGHCHRCSEPMFTIVYPKLFPLRETPMAGLHQGRTTVSF
          LYHTYH.FLKDLNFLSPISLPRSLLELLHCPLGHC.RCSEPMFTIVYPKLFPLRETPMAGLHQGRTTVSF
Retrocopy LYHTYHSFLKDLNFLSPISLPRSLLELLHCPLGHCLRCSEPMFTIVYPKLFPLRETPMAGLHQGRTTVSF

Parental  VAYCCSTQCLQTFDLLS
          VAYCCSTQCLQTFDLLS
Retrocopy VAYCCSTQCLQTFDLLS

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	1.62 RPM	10.94 RPM
SRP051959_heart	1.81 RPM	15.58 RPM
SRP051959_kidney	1.44 RPM	31.04 RPM
SRP051959_liver	1.82 RPM	27.83 RPM
SRP051959_lung	1.56 RPM	11.44 RPM
SRP051959_lymph_node	1.96 RPM	10.96 RPM
SRP051959_skeletal_muscle	1.42 RPM	12.34 RPM
SRP051959_spleen	2.21 RPM	13.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2430 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2430 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2430 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
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Callithrix jacchus	ENSCJAG00000016965	1 retrocopy	retro_cjac_2430 ,
Erinaceus europaeus	ENSEEUG00000006720	1 retrocopy	retro_eeur_672,
Monodelphis domestica	ENSMODG00000012729	1 retrocopy	retro_mdom_1822,
Ictidomys tridecemlineatus	ENSSTOG00000004380	1 retrocopy	retro_itri_1866,