RetrogeneDB ID: retro_cjac_2643

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:97719727..97720570(-)
• Located in intron of: ENSCJAG00000011265

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP2
• Ensembl ID: ENSCJAG00000021282
• Aliases: None
• Description: Nedd4 family interacting protein 2 [Source:HGNC Symbol;Acc:18537]

Sequence

>retro_cjac_2643
GGCAGCAGGAACAGAGGCAGAAGGGGTCCTGCAGCGACAGCGTTGTCAGCGGGGGTGGCCAAGGGAGCTGAGCACTGAGG
GGACTCGCCCACTCGGAAGCTGGATCCGGAGCCAGGCAGGATGGATCACCACCAGCCGGGGACTGGGCGCTACCGGGTGC
TTCTTAATGAAGAGGATAACTTAGAATCATTGGCCATAGAGCAGCCATCTACTTCAAACCCAGCAACACAGATTGTGCAG
GCTGCCTCTTCAGCACCAGCACTTGAAACTGACTCTTCACCTCCACCGTATAGTAGTATTACTGTGGAAGTACCTACAAC
TTCAGATACAGAAGTTTATGGTGAGTCTTATCCTGTGCCATCTCTCTATAGTGTTGCTGCCTCTCTTCCTACATACGATG
AAGCTGAGAAGGCTAAAGCTGCTGCAGTGGCAGATGCAGCAGAAACATCTCAAAGAATTCAGGAGAAAGAGTGTCCACCA
AGAGATGACTTCAGTGATGCAGACCAGCTCAGAGTGGGGAATAATGGCATTTTCATGCTGGCATTTTTCATGGCATTTAT
TTTCAACTGGCTTGGATTTTGTTTATTTTTCTGTATCACCAATACCATAGCTGGACAGTATGGTGCTATCTGCGGATTTG
GCCTTTCCTTGATCAAATGGATCCTTATTGTCAGGTTTTCTGATTATTTTACTGGATATTTCAATGGACAGTATTGGCTT
TGGTGGATATTTCTTGTACTTGGCCTGCTCCTTTTCTTCAGAGGATTCGTTAATTATCTAAAAGTCAGAAACATGTCTGA
AAGTATGGCAGCTGCTCATAGAACAACGTATTTCTTCTTCTTA

Alignment

ORF - retro_cjac_2643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.78 %
• Parental protein coverage: 83.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRNRGGRGPAATTLSAGVAEGAEHRGDSPARKPDPEPGRMDHHQPGTGRYQVLLNEEDNSESLAIEQPS
          G.RNRG.RGPAAT.LSAGVA.GAEH.GDSP.RK.DPEPGRMDHHQPGTGRY.VLLNEEDN.ESLAIEQPS
Retrocopy GSRNRGRRGPAATALSAGVAKGAEH*GDSPTRKLDPEPGRMDHHQPGTGRYRVLLNEEDNLESLAIEQPS

Parental  TSNTAPQIVQSASSAPALETDSSPPPYSSITVEVPTTSDTEVYSEFYPVPPPYSVATSLPTYDEAEKAKA
          TSN.A.QIVQ.ASSAPALETDSSPPPYSSITVEVPTTSDTEVY.E.YPVP..YSVA.SLPTYDEAEKAKA
Retrocopy TSNPATQIVQAASSAPALETDSSPPPYSSITVEVPTTSDTEVYGESYPVPSLYSVAASLPTYDEAEKAKA

Parental  AAMAAAAAETSQRIQEEECPPRDDFSDADQLRVGNDGIFMLAFFMAFIFNWLGFCLSFCITNTIAGRYGA
          AA.A.AA.ETSQRIQE.ECPPRDDFSDADQLRVGN.GIFMLAFFMAFIFNWLGFCL.FCITNTIAG.YGA
Retrocopy AAVADAA-ETSQRIQEKECPPRDDFSDADQLRVGNNGIFMLAFFMAFIFNWLGFCLFFCITNTIAGQYGA

Parental  ICGFGLSLIKWILIVRFSDYFTGYFNGQYWLWWIFLVLGLLLFFRGFVNYLKVRNMSESMAAAHRTRYFF
          ICGFGLSLIKWILIVRFSDYFTGYFNGQYWLWWIFLVLGLLLFFRGFVNYLKVRNMSESMAAAHRT.YFF
Retrocopy ICGFGLSLIKWILIVRFSDYFTGYFNGQYWLWWIFLVLGLLLFFRGFVNYLKVRNMSESMAAAHRTTYFF

Parental  LL
          .L
Retrocopy FL

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	0.07 RPM	23.01 RPM
SRP051959_heart	0.11 RPM	17.12 RPM
SRP051959_kidney	0.07 RPM	40.05 RPM
SRP051959_liver	0.09 RPM	26.86 RPM
SRP051959_lung	0.28 RPM	22.30 RPM
SRP051959_lymph_node	0.07 RPM	19.34 RPM
SRP051959_skeletal_muscle	0.04 RPM	26.07 RPM
SRP051959_spleen	0.15 RPM	27.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2643 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175,
Callithrix jacchus	ENSCJAG00000021282	2 retrocopies	retro_cjac_2643 , retro_cjac_2644,
Cavia porcellus	ENSCPOG00000014687	1 retrocopy	retro_cpor_753,
Loxodonta africana	ENSLAFG00000000864	1 retrocopy	retro_lafr_841,
Monodelphis domestica	ENSMODG00000001586	2 retrocopies	retro_mdom_1600, retro_mdom_48,
Mustela putorius furo	ENSMPUG00000003366	1 retrocopy	retro_mputfur_1079,
Tupaia belangeri	ENSTBEG00000005780	1 retrocopy	retro_tbel_3231,