RetrogeneDB ID: retro_cjac_4058

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:44681085..44681944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFF
• Ensembl ID: ENSCJAG00000012973
• Aliases: None
• Description: None

Sequence

>retro_cjac_4058
ATGGCAGAAATTAGTCAATTTCAGTATGAAATGGAATATAATAAAGATATTAGTCAGCAAATGAGGGCCCCAGAAAAATT
AAAGTTAGCACCATCAAATGGTGATCTGACACAAAAATTCCAAGAAGGAGTTCTAAATGCTAATGTGATGATGCGGATTC
TAGAGAGGATTGTTACAGCAGAGAACAACGGAGACATTCCAATTTGAAGACCAGTGGATCTTGACCTTATTCAGTCAACT
GCCTTTAAACCTCTGGCACTAAAACCACCACTTCATGTACTTTCAGTGAAAGACCACCAGATTTTCAGGATTTAAAAAGA
CCTTCAACCCTTCAAAATGAAGAAATCTGTGCAGTTGGCAAGCTAAAAAGAGACTGTTCTTTGACTGAAAATGTTGTTGG
CCGAAACAGACAGTTATCAGGAGTGATTTCATCGTGACACCATCACCATAAGAAGCTTGGATCTGCCTTCCCAAGATGAC
ACCCGAAAATAGAACTAATGTTTCCTCTGTTCATGGCCTCCTGTCATTTACCCAGTCTTCTACTCGTAGGGCTTACCAGC
ATATGGCGGATGCGCTAGATGAAAATCGCAGACCTGGTGCCAGCAGACCTGCTGGCACCACTTATCCTCAGCGGGACAAC
ATCAGGTATGGCACTTCAAATATAGATACAAGAACTGAAGGAACTTTGGATAACATGACTGTTGTAGATGCAGCTTCATT
AAGAAGACAGATAATCAAGCTAAATAGACGCTTACAACATCTGGAGGAAGAGAACAAAGAACGTGCCAAGAGAGAAATGG
TCATGTATTCAATTACCGTAGGATTCTGGCTGCTTAGTAGCTGGCTCTTGTTTCGTCGC

Alignment

ORF - retro_cjac_4058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEISRIQYEMEYTEGISQRMRVPEKLKVAPPNADLEQGFQEGVPNASVIMQVPERIVVAGNNEDASFSR
          MAEIS..QYEMEY...ISQ.MR.PEKLK.AP.N.DL.Q.FQEGV.NA.V.M...ERIV.A.NN.D....R
Retrocopy MAEISQFQYEMEYNKDISQQMRAPEKLKLAPSNGDLTQKFQEGVLNANVMMRILERIVTAENNGDIPI*R

Parental  PADLDLIQSTPFKPLALKTPPRVL-TLSERPLDFLDLERPATTPQNEEIRAVGRLKRERSMSENAVRQNG
          P.DLDLIQST.FKPLALK.PP....T.SERP.DF.DL.RP.T..QNEEI.AVG.LKR..S..EN.V..N.
Retrocopy PVDLDLIQSTAFKPLALK-PPLHV<TFSERPPDFQDLKRPSTL-QNEEICAVGKLKRDCSLTENVVGRNR

Parental  QL-VRNDSLVTPSPQQTRVCPPHMLPEDGANLSSARGILSLIQSSTRRAYQQILDVLDENRRPVLRGGSA
          QL..R.D..VTPSP.....C.P.M.PE...N.SS..G.LS..QSSTRRAYQ...D.LDENRRP.......
Retrocopy QL<IRSDFIVTPSP*EAWICLPKMTPENRTNVSSVHGLLSFTQSSTRRAYQHMADALDENRRP--GASRP

Parental  AATSNPHHDNVRYGISNIDSTIEGTSDDLTVVDAASLRRQIIKLNRRLQLLEEENKERAKREMVMYSITV
          A.T..P..DN.RYG.SNID...EGT.D..TVVDAASLRRQIIKLNRRLQ.LEEENKERAKREMVMYSITV
Retrocopy AGTTYPQRDNIRYGTSNIDTRTEGTLDNMTVVDAASLRRQIIKLNRRLQHLEEENKERAKREMVMYSITV

Parental  AFWLLNSWLWFRR
          .FWLL.SWL.FRR
Retrocopy GFWLLSSWLLFRR

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	0.04 RPM	30.84 RPM
SRP051959_heart	0.00 RPM	35.13 RPM
SRP051959_kidney	0.07 RPM	77.52 RPM
SRP051959_liver	0.00 RPM	23.85 RPM
SRP051959_lung	0.03 RPM	29.69 RPM
SRP051959_lymph_node	0.02 RPM	27.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	31.97 RPM
SRP051959_spleen	0.06 RPM	37.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4058 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4058 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4058 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021319	2 retrocopies	retro_btau_1233, retro_btau_826,
Callithrix jacchus	ENSCJAG00000012973	1 retrocopy	retro_cjac_4058 ,
Cavia porcellus	ENSCPOG00000011881	1 retrocopy	retro_cpor_803,
Homo sapiens	ENSG00000168958	2 retrocopies	retro_hsap_3391, retro_hsap_347,
Microcebus murinus	ENSMICG00000013200	1 retrocopy	retro_mmur_1002,
Nomascus leucogenys	ENSNLEG00000013420	1 retrocopy	retro_nleu_1706,