RetrogeneDB ID: retro_cjac_228

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:19385090..19386539(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022309
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021200
• Aliases: None
• Description: None

Sequence

>retro_cjac_228
GCGGTTCTGCTACCCGGGGTGCGGCGGCGGTTGTGGGGTTTCAGCGAGAGGCTGCTGATCCGAGGTGCTGCAGGACGGTC
ATCATATTTTGGAGAGAATAGATTGAGGAGTACACAGGCTGCTACACAAGTTGTTCTGAATGTTCCTGAAACAAGAGTAA
CATGTTTAGAAAGTGGACTTAGAGTGGCCTCTGAAGACTCTGGGCTCTCAACATGCACAGTTGGACTCTGGATTGATGCT
GGAAGTAGATATGAAAATGAGAAGAATAATGGAACAGCTCACTTTCTGGAGCATATGGCTTTCAAGGGCACCAAAAAGAG
ATCCCAGTTAGATTTGGAACTTGAGATTGAAAACATGGGTGCTCATCTCAATGCCTATACCTCCAGAGAGCAGACCGTAT
ACTATGCCAAAGCATTCTCTAAAGACTTGCCAAGAGCTGTAGAAATTCTTGCTGATATCATACAAAACAGCACACTGGGA
GAAGCAGAGATTGAACGTGAGCGTGGAGTAATCCTTAGAGAGATGCAAGAAGTTGAAACCAATTTACAAGAAGTTGTTTT
TGATTATCTTCATGCCACAGCTTATCAAAATACTGCACTTGGACGGACAATTTTGGGACCAACTGAAAATATCAAATCTA
TAAGTCGTAAGGACTTAGTGGATTATATAACCACACATTACAAGGGGCCAAGAATAGTTCTTGCTGCTGCTGGAGGTGTT
TCCCATGATGAATTGCTTGACTTAGCAAAGTTGCATTTTGGTGACTCTTTATGCACACACAAAGGAGAAATACCAGCTCT
GCCTCCCTGCAAATTCACAGGAAGTGAGATTCGTATGAGGGATGACAAGATGCCTTTGGCACACCTTGCAATAGCTGTTG
AAGCTGTTGGTTGGGCACATCCAGATACAATATGTCTTATGGTTGCAAACACGCTGATTGGCAACTGGGATCGCTCTTTT
GGAGGAGGAATGAATTTATCTAGCAAGCTGGCCCAGCTCACTTGTCAGGGCAACCTTTGCCATAGCTTTCAGTCTTTCAA
CACTTCCTACACAGATACAGGATTATGGGGACTGTATATGGTTTGTGAACCAGCCACCGTTGGAGACATGCTACATGTTG
TTCAGAAAGAATGGATGCGACTCTGTACAAGTGTCACTGAAAGTGAGGTTGCACGAGCCAGAAATCTTCTGAAAACAAAC
ATGTTGTTGCAGCTTGATGGTTCAACTCCAATTTGTGAAGATATTGGTAGGCAGATGTTATGCTATAATAGAAGGATTCC
CATCCCTGAGCTTGAAGTAAGAATTGATGCTGTGAATGCTGAGACAATTCGAGAAGTATGTACCAAATATATTTATAATA
AGAGTCCAGCTATTGCTGCTGTTGGTCCCATTGAGCAACTACCAGATTTTAATCAGATTTGCAGTAACATGTGTTGGCTT
CGTGATTAA

Alignment

ORF - retro_cjac_228 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 98.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVLLPGVRRRLWGFSERLLIRGAAGRSSYFGENRLRSTQAATQVVLNVPETRVTCLESGLRVASEDSGLS
          AVLLPGVRRRLWGFSERLLIRGAAGRSSYFGENRLRSTQAATQVVLNVPETRVTCLESGLRVASEDSGLS
Retrocopy AVLLPGVRRRLWGFSERLLIRGAAGRSSYFGENRLRSTQAATQVVLNVPETRVTCLESGLRVASEDSGLS

Parental  TCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFS
          TCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFS
Retrocopy TCTVGLWIDAGSRYENEKNNGTAHFLEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFS

Parental  KDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTEN
          KDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTEN
Retrocopy KDLPRAVEILADIIQNSTLGEAEIERERGVILREMQEVETNLQEVVFDYLHATAYQNTALGRTILGPTEN

Parental  IKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKLHFGDSLCTHKGEIPALPPCKFTGSEIRMR
          IKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKLHFGDSLCTHKGEIPALPPCKFTGSEIRMR
Retrocopy IKSISRKDLVDYITTHYKGPRIVLAAAGGVSHDELLDLAKLHFGDSLCTHKGEIPALPPCKFTGSEIRMR

Parental  DDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCQGNLCHSFQSFNTSY
          DDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCQGNLCHSFQSFNTSY
Retrocopy DDKMPLAHLAIAVEAVGWAHPDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCQGNLCHSFQSFNTSY

Parental  TDTGLWGLYMVCEPATVGDMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQML
          TDTGLWGLYMVCEPATVGDMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQML
Retrocopy TDTGLWGLYMVCEPATVGDMLHVVQKEWMRLCTSVTESEVARARNLLKTNMLLQLDGSTPICEDIGRQML

Parental  CYNRRIPIPELEVRIDAVNAETIREVCTKYIYNKSPAIAAVGPIEQLPDFNQICSNMCWLRD
          CYNRRIPIPELEVRIDAVNAETIREVCTKYIYNKSPAIAAVGPIEQLPDFNQICSNMCWLRD
Retrocopy CYNRRIPIPELEVRIDAVNAETIREVCTKYIYNKSPAIAAVGPIEQLPDFNQICSNMCWLRD

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	12.34 RPM
SRP051959_heart	0.05 RPM	19.29 RPM
SRP051959_kidney	0.09 RPM	25.14 RPM
SRP051959_liver	0.09 RPM	19.95 RPM
SRP051959_lung	0.05 RPM	14.53 RPM
SRP051959_lymph_node	0.09 RPM	16.37 RPM
SRP051959_skeletal_muscle	0.02 RPM	24.63 RPM
SRP051959_spleen	0.06 RPM	14.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_228 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_228 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	ENSCJAG00000003132	1 retrocopy	retro_cjac_2204,
Callithrix jacchus	ENSCJAG00000021200	1 retrocopy	retro_cjac_228 ,
Myotis lucifugus	ENSMLUG00000008798	1 retrocopy	retro_mluc_43,
Rattus norvegicus	ENSRNOG00000012693	1 retrocopy	retro_rnor_2963,
Tursiops truncatus	ENSTTRG00000010699	1 retrocopy	retro_ttru_1171,