RetrogeneDB ID: retro_cjac_3295

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:39737014..39737859(-)
• Located in intron of: ENSCJAG00000021157

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EMC2
• Ensembl ID: ENSCJAG00000006437
• Aliases: None
• Description: ER membrane protein complex subunit 2 [Source:HGNC Symbol;Acc:28963]

Sequence

>retro_cjac_3295
GAAATGCAAGATAAAATGAGAAAATGGAGAGAAGAAAACTCATGAGATACTGAGCAAATTGTGGAAGTTGGAGAAGAATT
AATTAATGAATATGCTTCTAAGCTTGGAGATGCTATTTGGATGATATATGAACAGGTGATGATTGCTGCTCTAGACTACG
GTCGGGATGACTTGGCACTGTTTTGTCTTCAAGAGTTAAGACAGTTCCCTGGCAGTCACAGAGTCAAGCGATTAACAGGC
ATGAGATCTGAAGCCATGGAAAGACATGATGATGCTATCCAGCTATATGATAGGATTTTACAAGAAGATCCAACTAACAC
CGCTGCAAGAAAGCATTAAGATTGCCGTTCGAAAAGCCCAGGGGAAAAACGTGGAGGCCGTTCGGGAACTGAATGAGTGT
CTGGAACAATTTGTTGGAGACCAAGAAGCCTGGCATGAACTTGCAGAACATTATATCAATGAACATGACTATGCAAAAGC
AGCCTTTTGTTTAGAGGAACTAATGATGACTAATCCACACAACCACTGTTGTCAGCAGTATGCTGAAGTTAAATATACCA
CCCAAGGTGGACTTGAAAACCTCGAACTTTCAAGAAAGTGTTGTGCGCAGGCATTGAAACTGAGCAACAGAAATGTGAGA
GCTTTGGGCTTCCTATGTCGGCAAGTCATATTGCTTCTAATCCAAAAGCAAATGCAAAAACGAAAAAGGACAACATGAAT
TATCCTAGTTGGGCAGCTGGTCAAATGACAGAGCTTATCAGTTTGCAGGTCGAAGCAAGAGGGAAATCAAATATTTCCTT
AATGCAGTCGAAGACATGTTGGAAAAATTACAGATCACCCAGTCT

Alignment

ORF - retro_cjac_3295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 95.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRDDLALFCLQELRRQF
          EM.DKMRKWREENS...EQIVEVGEELINEYASKLGD.IW.IYEQVMIAALDYGRDDLALFCLQELR.QF
Retrocopy EMQDKMRKWREENS*DTEQIVEVGEELINEYASKLGDAIWMIYEQVMIAALDYGRDDLALFCLQELR-QF

Parental  PGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKR-KIAIRKAQGKNVEAIRELNEYLEQFV
          PGSHRVKRLTGMR.EAMER.DDAIQLYDRILQEDPTNTAARK..KIA.RKAQGKNVEA.RELNE.LEQFV
Retrocopy PGSHRVKRLTGMRSEAMERHDDAIQLYDRILQEDPTNTAARKH>KIAVRKAQGKNVEAVRELNECLEQFV

Parental  GDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYT-QGGLENLELS-RKYFAQALK
          GDQEAWHELAE.YINEHDYAKAAFCLEELMMTNPHNH..CQQYAEVKYT.QGGLENLELS..K.......
Retrocopy GDQEAWHELAEHYINEHDYAKAAFCLEELMMTNPHNHC-CQQYAEVKYTTQGGLENLELS<KKVLCAGIE

Parental  LNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQI-NRAYQFAGRSKKETKYSLKAVEDML
          .........FGL.MSASHIASNPKA.AKTKKDNM.Y.SWAA.Q...RAYQFAGRSK.E.KY.L.AVEDML
Retrocopy TEQQKCES-FGLPMSASHIASNPKANAKTKKDNMNYPSWAAGQM<DRAYQFAGRSKREIKYFLNAVEDML

Parental  ETLQITQS
          E.LQITQS
Retrocopy EKLQITQS

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	13.84 RPM
SRP051959_heart	0.00 RPM	22.10 RPM
SRP051959_kidney	0.00 RPM	23.30 RPM
SRP051959_liver	0.00 RPM	19.02 RPM
SRP051959_lung	0.00 RPM	23.03 RPM
SRP051959_lymph_node	0.02 RPM	16.37 RPM
SRP051959_skeletal_muscle	0.00 RPM	20.46 RPM
SRP051959_spleen	0.00 RPM	21.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3295 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3295 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012826	1 retrocopy	retro_amel_600,
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726,
Choloepus hoffmanni	ENSCHOG00000011271	3 retrocopies	retro_chof_1512, retro_chof_1990, retro_chof_851,
Callithrix jacchus	ENSCJAG00000006437	2 retrocopies	retro_cjac_3295 , retro_cjac_3867,
Myotis lucifugus	ENSMLUG00000013258	2 retrocopies	retro_mluc_2369, retro_mluc_2452,
Mustela putorius furo	ENSMPUG00000005915	1 retrocopy	retro_mputfur_1647,
Mus musculus	ENSMUSG00000022337	1 retrocopy	retro_mmus_1262,
Oryctolagus cuniculus	ENSOCUG00000002461	1 retrocopy	retro_ocun_1251,
Pongo abelii	ENSPPYG00000018820	1 retrocopy	retro_pabe_1600,