RetrogeneDB ID: retro_rnor_2779

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:23834160..23834632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab7a
• Ensembl ID: ENSRNOG00000012247
• Aliases: Rab7a, Rab7
• Description: Ras-related protein Rab-7a [Source:UniProtKB/Swiss-Prot;Acc:P09527]

Sequence

>retro_rnor_2779
GTGATGGTGGATTACAGAATTGTTACCGTGTGGATCTGGGATACAGCTGGTCAAGAATGGTTCCAGTCTCTTGGTGTGGC
CTTCTACACAGGTACAGATTGCTGCATTCTGGTGTTTGATATGACTGCCTCCAACACATTCAAAACCCTGGACAGCAAAA
GAGACAAATTTCTTATTCAGGCCAGCACCTAGGAGCCAAAGAACTTCCCTTTTGTGTTGGGAAACAAAATTGACCTCAAA
GACAAGACATGTGGCCACAAAGAGGGTATGGGCTTGGTGCTACAGAGCAAACAATATTCACTGCTTCAAGACCATTGCCA
AAGAGTTCATCAATGTGGAGCAGGCTTTTCAGACAATTGCTCAGAACACCCTTAAGCAGGAAACAGAAGTCGAGCTATAC
AATGAATTCCCTGAACCCGTCAAGCTAGACAAGAATGACTCAGCCAATGCCTCTGATGAGAGATGAAGTTGT

Alignment

ORF - retro_rnor_2779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.47 %
• Parental protein coverage: 76.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFP
          VMVD.R.VT..IWDTAGQE.FQSLGVAFY.G.DCC.LVFD.TA.NTFKTLDS.RD.FLIQAS...P.NFP
Retrocopy VMVDYRIVTVWIWDTAGQEWFQSLGVAFYTGTDCCILVFDMTASNTFKTLDSKRDKFLIQAST*EPKNFP

Parental  FVVLGNKIDLEN-RQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPE
          F.VLGNKIDL...R.VATKR..AWCY..NNI..F.T.AKE.INVEQAFQTIA.N.LKQETEVELYNEFPE
Retrocopy F-VLGNKIDLKD>RHVATKRVWAWCYRANNIHCFKTIAKEFINVEQAFQTIAQNTLKQETEVELYNEFPE

Parental  PIKLDKNERAKASAESCSC
          P.KLDKN..A.AS.E..SC
Retrocopy PVKLDKNDSANASDER*SC

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	189.16 RPM
SRP017611_kidney	0.00 RPM	234.89 RPM
SRP017611_liver	0.00 RPM	144.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2779 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2779 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000365	1 retrocopy	retro_chof_13,
Felis catus	ENSFCAG00000022971	2 retrocopies	retro_fcat_661, retro_fcat_76,
Meleagris gallopavo	ENSMGAG00000007208	1 retrocopy	retro_mgal_7,
Myotis lucifugus	ENSMLUG00000008454	1 retrocopy	retro_mluc_1641,
Mustela putorius furo	ENSMPUG00000017333	1 retrocopy	retro_mputfur_1169,
Mus musculus	ENSMUSG00000079477	2 retrocopies	retro_mmus_3339, retro_mmus_3546,
Oryctolagus cuniculus	ENSOCUG00000001645	1 retrocopy	retro_ocun_259,
Pongo abelii	ENSPPYG00000013431	1 retrocopy	retro_pabe_90,
Rattus norvegicus	ENSRNOG00000012247	1 retrocopy	retro_rnor_2779 ,
Sarcophilus harrisii	ENSSHAG00000016787	1 retrocopy	retro_shar_65,