RetrogeneDB ID: retro_rnor_1135

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:10496915..10497197(-)
• Located in intron of: ENSRNOG00000014661

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sft2d2
• Ensembl ID: ENSRNOG00000003038
• Aliases: None
• Description: Vesicle transport protein SFT2B [Source:UniProtKB/Swiss-Prot;Acc:Q4FZV2]

Sequence

>retro_rnor_1135
GGCCTCTTTGCAGTGTTTTATACCCTGGGTAACATTACATCAACTGGGAGTTCCATCTTCCTTACGGGGCCAGTGAAGCA
GCTGAAGTGTATGTTTGAGCATCTCATTGCCATAATACTGGTGCTGTTGTGTTTTGCACTTACCCTGTGCTCTGCCTTTT
AGTGGAATAAGGAACTTGGACTCATCTTCTATATTTTGCAGTATTTGGCTTAGAGGTGGTATAGGCTTTCCTACATACCA
TATGCGAGGGATGCTGTGAAGAAGTGCTGTGCTGCGTGTCTT

Alignment

ORF - retro_rnor_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.08 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLFAVFYTLGNITSIGSTMFLMGPLKQLKRMFEPTRLIATILVLLFFVLTLCSAFLWNKGLALIFCILQS
          GLFAVFYTLGNITS.GS..FL.GP.KQLK.MFE...LIA.ILVLL.F.LTLCSAF.WNK.L.LIF.ILQ.
Retrocopy GLFAVFYTLGNITSTGSSIFLTGPVKQLKCMFE--HLIAIILVLLCFALTLCSAF*WNKELGLIFYILQY

Parental  LALTWYSLSYIPYARDAVKKCFAVCL
          LA..WY.LSYIPYARDAVKKC.A.CL
Retrocopy LA*RWYRLSYIPYARDAVKKCCAACL

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
SRP017611_brain	0.00 RPM	1.65 RPM
SRP017611_kidney	0.00 RPM	20.45 RPM
SRP017611_liver	0.00 RPM	11.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1135 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010720	1 retrocopy	retro_acar_131,
Callithrix jacchus	ENSCJAG00000016838	1 retrocopy	retro_cjac_2771,
Monodelphis domestica	ENSMODG00000002896	1 retrocopy	retro_mdom_607,
Mustela putorius furo	ENSMPUG00000000531	1 retrocopy	retro_mputfur_1560,
Nomascus leucogenys	ENSNLEG00000014912	1 retrocopy	retro_nleu_2370,
Rattus norvegicus	ENSRNOG00000003038	1 retrocopy	retro_rnor_1135 ,
Sarcophilus harrisii	ENSSHAG00000018938	1 retrocopy	retro_shar_212,
Ictidomys tridecemlineatus	ENSSTOG00000022560	1 retrocopy	retro_itri_133,