RetrogeneDB ID: retro_cjac_1960

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:133035559..133036234(-)
• Located in intron of: ENSCJAG00000016954

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB4
• Ensembl ID: ENSCJAG00000004020
• Aliases: None
• Description: MOB family member 4, phocein [Source:HGNC Symbol;Acc:17261]

Sequence

>retro_cjac_1960
GTGGTCATGGTGGAGGGGACTGCAGTTCTGAGGTGGAACAGGCCGGGCACCAAGGCGCAGGATTTCTATAATTGGCCTGA
TGAATCCTTTGATGAAATGGACAGTACACTAGCTGTTCAACAGTATATTCAACAGAATATAAGAGCTGATTGCTCCAATA
TTGACAAAATTCTTGAACCACCTGAAGGCCAAGATGAAGGTTTATGGAAGTATGAACATTTAAGGTAATTCTGCCTTGAG
CTAAATGGACTTGCTGTCAAACTTCAGAGCAAATGCCATCCAGATACTTGCACTCAAATGACAGCAACTGAACAATGGAT
TTTTCTTTGTGCAGCTCATAAAACTCCAAAAGAGTGTCCTGCTATTGACTACACTAGACACACATTTGATGGTGCTGCAT
GTCTTCTGAATAGCAATAAATATTTTCCCAGCAGGGTTAGCATAAAGGAACCATCTGTAGCGAAACTAGGATCAGTATGC
CGTAGGATTTACAAAATATTTTCACATGCTTATTTTCATCATCGGCAGATATTTGATGAATATGAAAATGAAACATTTTT
GTGTCATTGGTTTACTAAATTTGTGATGAAATATAATTTGATGTCCAAGGATAACCTGATTGTACCAATTTTAGAAGAGG
AAGTACAGAATTCAGTTTCTGGGGAAAGTGAAGCA

Alignment

ORF - retro_cjac_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVMAEGTAVLRRNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEGVWK
          .VM.EGTAVLR.NRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEG.WK
Retrocopy VVMVEGTAVLRWNRPGTKAQDFYNWPDESFDEMDSTLAVQQYIQQNIRADCSNIDKILEPPEGQDEGLWK

Parental  YEHLRQFCLELNGLAVKLQSECHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTLDGAACLLNSNK
          YEHLR.FCLELNGLAVKLQS.CHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHT.DGAACLLNSNK
Retrocopy YEHLR*FCLELNGLAVKLQSKCHPDTCTQMTATEQWIFLCAAHKTPKECPAIDYTRHTFDGAACLLNSNK

Parental  YFPSRVSIKESSVAKLGSVCRRIYRIFSHAYFHHRQIFDEYENETFLCHRFTKFVMKYNLMSKDNLIVPI
          YFPSRVSIKE.SVAKLGSVCRRIY.IFSHAYFHHRQIFDEYENETFLCH.FTKFVMKYNLMSKDNLIVPI
Retrocopy YFPSRVSIKEPSVAKLGSVCRRIYKIFSHAYFHHRQIFDEYENETFLCHWFTKFVMKYNLMSKDNLIVPI

Parental  LEEEVQNSVSGESEA
          LEEEVQNSVSGESEA
Retrocopy LEEEVQNSVSGESEA

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	4.99 RPM	19.26 RPM
SRP051959_heart	0.70 RPM	20.35 RPM
SRP051959_kidney	0.84 RPM	17.64 RPM
SRP051959_liver	7.97 RPM	11.31 RPM
SRP051959_lung	1.01 RPM	17.70 RPM
SRP051959_lymph_node	1.19 RPM	16.60 RPM
SRP051959_skeletal_muscle	0.20 RPM	15.02 RPM
SRP051959_spleen	1.09 RPM	17.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1960 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004020	2 retrocopies	retro_cjac_1960 , retro_cjac_3238,
Cavia porcellus	ENSCPOG00000012746	2 retrocopies	retro_cpor_318, retro_cpor_804,
Homo sapiens	ENSG00000115540	2 retrocopies	retro_hsap_2275, retro_hsap_906,
Gorilla gorilla	ENSGGOG00000009005	2 retrocopies	retro_ggor_733, retro_ggor_743,
Latimeria chalumnae	ENSLACG00000015430	1 retrocopy	retro_lcha_112,
Macaca mulatta	ENSMMUG00000016547	1 retrocopy	retro_mmul_829,
Monodelphis domestica	ENSMODG00000012305	2 retrocopies	retro_mdom_1333, retro_mdom_963,
Oryctolagus cuniculus	ENSOCUG00000005712	1 retrocopy	retro_ocun_30,
Otolemur garnettii	ENSOGAG00000000272	1 retrocopy	retro_ogar_2739,
Ochotona princeps	ENSOPRG00000016650	2 retrocopies	retro_opri_444, retro_opri_812,
Pongo abelii	ENSPPYG00000013047	6 retrocopies	retro_pabe_1943, retro_pabe_2021, retro_pabe_3600, retro_pabe_781, retro_pabe_795, retro_pabe_970,
Sarcophilus harrisii	ENSSHAG00000017821	1 retrocopy	retro_shar_351,
Ictidomys tridecemlineatus	ENSSTOG00000021024	1 retrocopy	retro_itri_727,
Tarsius syrichta	ENSTSYG00000001726	1 retrocopy	retro_tsyr_1673,