RetrogeneDB ID: retro_cjac_855

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:53787192..53788293(+)
• Located in intron of: ENSCJAG00000014492

Retrocopy information

• Ensembl ID: ENSCJAG00000014543
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSCJAG00000011009
• Aliases: None
• Description: None

Sequence

>retro_cjac_855
ATGAGCAGCACCTTAGCTAAGATCGCGGAGATAGAAGCTGAGATGGCTCGGACTCAAAAGAACAAGGCCACAGCACACCA
CCTAGGGCTGCTTAAGGCTCGTCTTGCTAAGCTTCGTCGAGAACTCATTACTCCAAAGGGTGGTGGTGGTGGAGGTCCAG
GAGAAGGTTTTGATGTGGCCAAGACAGGTGATGCTCGAATTGGATTTGTTGGTTTTCCATCTGTGGGGAAGTCAACACTG
CTTAGTAACCTGGCAGGGGTGTATTCTGAGGTAGCAGCCTATTGAATTCACTACTCTGACCACCATGCCTGGTGTCATCA
GATACAAAGGTGCCAAGATCCAGCTCCTGGATCTCCCAGGTATCATTGAAAGTGCCAAGGATGGGAAAGGTAGAGGTCAT
CAAGTCATTGCAGTGGCCCGAACCTGTAACTTGATCCTGATTGTTTTGGATGTCCTGAAACCCTTGGGACATAAGAAGAT
AATTGAAAATGAACTGGAAGGCTTTGGCATTCGCTTGAACAGCAAACCCCCCAACATTGGCTTTAAGAAAAAGGACAAGG
GAGGCATTAATCTCACAGCTACTTGCCCCCAGAGTGAGCTGAATGCTGAAACTGTGAAAAGCATTCTGGCCAAATACAAG
ATTCATAATGCTGATGTGACTCTACGTAGTGATGCTACAGCTGTGACCTCATTGATGTGGTGGAAGGAAACAGAGTTTAT
ATCCCCTGTATCTATGTGTTAAATAAGATTGACCAAATCTCCATTGAGGAATTGGATATCATCTATAAGGTGCCTCACTG
TGTATTCATCTCTGCCCATCACTGTTGGAATTTTGATGACCTATTGGAAAAGATCTGGGACTATCTGAAACTAGTGAGAA
TTTACACCAAACCCAAAGGCCAGTTACCAGATTACATATCCCCAGTGGTGCTTCCTTACTCCAGGACCACAGTGGAGGAT
TTCTGCATGAAGATTCACAAAAATCTTATCAAAGAATTTAAATATGCTCTGGTCTGGGGTCTCTCTGTGAAACACAATCC
TCAGAAAGTGGGTAAAGACCATACGTTGGAGGATGAGGATGTCATTCAAATTGTGAAGAAG

Alignment

ORF - retro_cjac_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
          MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
Retrocopy MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV

Parental  GFPSVGKSTLLSNLAGVYSEVAAY-EFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVA
          GFPSVGKSTLLSNLAGVYSEVAAY.EFTTLTT.PGVIRYKGAKIQLLDLPGIIE.AKDGKGRG.QVIAVA
Retrocopy GFPSVGKSTLLSNLAGVYSEVAAY>EFTTLTTMPGVIRYKGAKIQLLDLPGIIESAKDGKGRGHQVIAVA

Parental  RTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDAETVKSIL
          RTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSEL.AETVKSIL
Retrocopy RTCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELNAETVKSIL

Parental  AEYKIHNADVTLRSDATAD-DLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVPISAHHRWNF
          A.YKIHNADVTLRSDATA..DLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCV.ISAHH.WNF
Retrocopy AKYKIHNADVTLRSDATAV<DLIDVVEGNRVYIPCIYVLNKIDQISIEELDIIYKVPHCVFISAHHCWNF

Parental  DDLLEKIWDYLKLVRIYTKPKGQLPDYTSPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQ
          DDLLEKIWDYLKLVRIYTKPKGQLPDY.SPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQ
Retrocopy DDLLEKIWDYLKLVRIYTKPKGQLPDYISPVVLPYSRTTVEDFCMKIHKNLIKEFKYALVWGLSVKHNPQ

Parental  KVGKDHTLEDEDVIQIVKK
          KVGKDHTLEDEDVIQIVKK
Retrocopy KVGKDHTLEDEDVIQIVKK

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	12.89 RPM
SRP051959_heart	0.25 RPM	12.47 RPM
SRP051959_kidney	0.04 RPM	15.18 RPM
SRP051959_liver	0.04 RPM	12.93 RPM
SRP051959_lung	0.10 RPM	12.97 RPM
SRP051959_lymph_node	0.02 RPM	14.47 RPM
SRP051959_skeletal_muscle	0.02 RPM	17.67 RPM
SRP051959_spleen	0.00 RPM	15.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_855 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_855 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104, retro_cjac_2246, retro_cjac_2606, retro_cjac_855 ,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,