RetrogeneDB ID: retro_cjac_292

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:25473632..25474628(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022707
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019154
• Aliases: None
• Description: None

Sequence

>retro_cjac_292
ATGGATTGGGTTATGAAACATAATGGTCCAAATGACGCTAGAGATGGGACAGTAAGACTTCGTGGACTACCATTTGGTTG
CAGCAAAGAGGAAATAGTTCAGTTCTTTCAAGGGTTGGAAATCGTGCCAAATGGGATAACATTGATGATGGACTACCAGG
GGAGAAGCACAGGGGAGGCCTTCGTGCAGTTTGCTTCAAAGGAGATAACAGAAAATGCTCTGGGGAAACACAAGGAAAGA
ATAGGGCACAGGTATATTGAGATCTTCAGAAGTAGCAGGAATGAAATCGAAGGATTTTATGATCCACCAAAAAGATTGCT
GGGACAGCGACCGGGACCATATGATAGACCAATAGGAGGAAGAGGGGGTTATTATGGAGCTGGGTGTGGAAGTTATGGAG
GTTTTGATGACTATGGTGGCTATAATAATTATGGCTATGGGAATGATGGCTTTGATGACAGAATGAGAGATGGAAGAGGT
ATGGGAGGGCATGGCTATGGTGGAGCTGGTGATGCAAGTTCAGGTTTTCATGGTGGTCATTTCGTACATATGAGAGGGTT
GCCTTTTCGTGCAACTGAAAATGACATTGCTAATTTCTTCTCACCATTAAATCCAATACGAGTTCATATTGATATTGGAG
CTGATGGCAGAGCCACAGGAGAAGCAGATGTAGAGTTTGTGACACATGAAGATGCAGTAGCTGCCATGTCTAAAGATAAA
AATAACATGCAACATCAATATATTGAACTCTTCTTGAATTCTACTCCTGCAGGTGGCTCTGGCATGGGAGGTTCTGGAAT
GGGAGGCTATGGAAGAGATGGAATGGATAATCAGGGAGGTTATGGATCACTTGGAAGAATGGGAATGGGGAACAATTACA
GTGGAGGATATGGTACTCCTGATGGCTTGGGTGGTTATGCCCGTGGTGGTGGAGGCAGTGGAGGTTACCACGGGCAAGGT
GGCATGAGTGGAGGTGGATGGCGTGGGATGTACTGA

Alignment

ORF - retro_cjac_292 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.03 %
• Parental protein coverage: 93.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGYGGFDDYGGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANF
          G.YGGFDDYGGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANF
Retrocopy GSYGGFDDYGGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANF

Parental  FSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHRYIELFLNSTPGGGSGMGGSGMGG
          FSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQH.YIELFLNSTP.GGSGMGGSGMGG
Retrocopy FSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNNMQHQYIELFLNSTPAGGSGMGGSGMGG

Parental  YGRDGMDNQGGYGSVGRMGMGNNYSGGYGTPDGLGGYGRGGGGSGGYYGQGGMSGGGWRGMY
          YGRDGMDNQGGYGS.GRMGMGNNYSGGYGTPDGLGGY.RGGGGSGGY.GQGGMSGGGWRGMY
Retrocopy YGRDGMDNQGGYGSLGRMGMGNNYSGGYGTPDGLGGYARGGGGSGGYHGQGGMSGGGWRGMY

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	0.22 RPM	19.46 RPM
SRP051959_heart	0.35 RPM	28.63 RPM
SRP051959_kidney	0.29 RPM	24.69 RPM
SRP051959_liver	0.09 RPM	15.92 RPM
SRP051959_lung	0.37 RPM	34.32 RPM
SRP051959_lymph_node	0.41 RPM	38.93 RPM
SRP051959_skeletal_muscle	0.15 RPM	13.61 RPM
SRP051959_spleen	0.36 RPM	32.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_292 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_292 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_292 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000009931	1 retrocopy	retro_cjac_127,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292 , retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,