RetrogeneDB ID: retro_cjac_67

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:84099581..84100508(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000008253
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005282
• Aliases: None
• Description: None

Sequence

>retro_cjac_67
ATGGGAGAGATTAAAGTCTCTCCTGATTATAACTGGTTTAGAGGTTCAGTTCCCCTTAAAAAGATTATCGTAGATGATGA
TGACAGTAAGATATGGTCGCTCTATGATGCGGGTCCCCGAAGTATCAGGTGTCCTCTGATATTCCTGCCTCCTGTCAGTG
GAACTGCAGATGTCTTTTTCCGGCAGATTTTGGCTCTGACTGGATGGGGTTACCGGGTTATCGCTTTGCAGTATCCAGTT
TATTGGGACCATCTCGAATTCTGTGATGGATTCAGAAAACTTTTAGACCATTTACAATTGGATAAAGTTCATCTTTTTGG
CGCTTCTTTGGGAGGCTTTTTGGCCCAGAAATTTGCTGAATACACTCACAAATCTCCGAGAGTCCATTCCCTCATCCTCT
GCAATTCCTTCAGTGACACCTCTATCTTCAACCAAACTTGGACTGCAAACAGCTTTTGGCTGATGCCAGCATTTATGCTC
AAAAAGATAGTTCTTGGAAACTTTTCATCTGGCCCAGTGGACCCTATGATGGCTGATGCCATTGATTTCATGGTAGACAG
GCTAGAAAGTTTGGGTCAGAGTGAACTGGCTTCAAGACTTACCTTGAACTGTCAAAATTCTTATGTGGAACCTCATAAAA
TTCGGGACATCCCTGTAACCATTATGGACGTGTTTGATCAGAGTGCACTTTCAACTGAAGCTAAAGAAGAAATGTACAAG
CTGTATCCTAATGCCCGAAGAGCTCACCTTAAAACAGGAGGCAATTTCCCATACCTGTGCAGAAGTGCAGAGGTGAATCT
TTATGTACAGATACATTTGTTGCAATTCCATGGAACCAAATACGCGGCCATTGACCCATCAATGGTCAGTGCGGAGGAGC
TTGAGGTGCAGAAAGGCAGCCTCGGCATCAGCCAGGAAGAACAATAG

Alignment

ORF - retro_cjac_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MGEIKVSPDYNWFRGSVPLKKIIVDDDDSKIWSLYDAGPRSIRCPLIFLPPVSGTADVFFRQILALTGWG
          MGEIKVSPDYNWFRGSVPLKKIIVDDDDSKIWSLYDAGPRSIRCPLIFLPPVSGTADVFFRQILALTGWG
Retrocopy MGEIKVSPDYNWFRGSVPLKKIIVDDDDSKIWSLYDAGPRSIRCPLIFLPPVSGTADVFFRQILALTGWG

Parental  YRVIALQYPVYWDHLEFCDGFRKLLDHLQLDKVHLFGASLGGFLAQKFAEYTHKSPRVHSLILCNSFSDT
          YRVIALQYPVYWDHLEFCDGFRKLLDHLQLDKVHLFGASLGGFLAQKFAEYTHKSPRVHSLILCNSFSDT
Retrocopy YRVIALQYPVYWDHLEFCDGFRKLLDHLQLDKVHLFGASLGGFLAQKFAEYTHKSPRVHSLILCNSFSDT

Parental  SIFNQTWTANSFWLMPAFMLKKIVLGNFSSGPVDPMMADAIDFMVDRLESLGQSELASRLTLNCQNSYVE
          SIFNQTWTANSFWLMPAFMLKKIVLGNFSSGPVDPMMADAIDFMVDRLESLGQSELASRLTLNCQNSYVE
Retrocopy SIFNQTWTANSFWLMPAFMLKKIVLGNFSSGPVDPMMADAIDFMVDRLESLGQSELASRLTLNCQNSYVE

Parental  PHKIRDIPVTIMDVFDQSALSTEAKEEMYKLYPNARRAHLKTGGNFPYLCRSAEVNLYVQIHLLQFHGTK
          PHKIRDIPVTIMDVFDQSALSTEAKEEMYKLYPNARRAHLKTGGNFPYLCRSAEVNLYVQIHLLQFHGTK
Retrocopy PHKIRDIPVTIMDVFDQSALSTEAKEEMYKLYPNARRAHLKTGGNFPYLCRSAEVNLYVQIHLLQFHGTK

Parental  YAAIDPSMVSAEELEVQKGSLGISQEEQ
          YAAIDPSMVSAEELEVQKGSLGISQEEQ
Retrocopy YAAIDPSMVSAEELEVQKGSLGISQEEQ

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	0.09 RPM	9.74 RPM
SRP051959_heart	0.09 RPM	9.49 RPM
SRP051959_kidney	0.20 RPM	16.40 RPM
SRP051959_liver	0.09 RPM	16.14 RPM
SRP051959_lung	0.11 RPM	12.44 RPM
SRP051959_lymph_node	0.16 RPM	14.68 RPM
SRP051959_skeletal_muscle	0.07 RPM	6.40 RPM
SRP051959_spleen	0.19 RPM	15.57 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_67 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_67 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_67 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005282	1 retrocopy	retro_cjac_67 ,
Macropus eugenii	ENSMEUG00000013791	1 retrocopy	retro_meug_116,
Oryctolagus cuniculus	ENSOCUG00000016136	1 retrocopy	retro_ocun_204,
Otolemur garnettii	ENSOGAG00000010385	1 retrocopy	retro_ogar_3249,
Ictidomys tridecemlineatus	ENSSTOG00000010101	1 retrocopy	retro_itri_1397,