RetrogeneDB ID: retro_rnor_2744

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:86003609..86004229(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000027719
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rab18
• Ensembl ID: ENSRNOG00000018972
• Aliases: None
• Description: Ras-related protein Rab-18 [Source:UniProtKB/Swiss-Prot;Acc:Q5EB77]

Sequence

>retro_rnor_2744
ATGGACGAGGACGAGCTGACCACTCTGAAGATCCTCATCATCGGCAAGAGTGGGGTGGGCAAGTCCAGCCTGCTCCTGAG
GTTCACAGACAACACCTTTGATCCAGAACTTGCAGCAACAATAGGTGTTGACTTTAAGGTGAAAACGATTTCAGTGGATG
GAAATAAGGCTAAACTTGCAATATGGGATACAGCTGGCCAAGAAAGGTTCAGAACATTAACTCCCAGCTATTATAGAGGT
GCACAGGGAGTTATATTAGTCTATGATGTCACAAGAAGAGACACCTTTGTTAAACTGTATAATTGGTTAAATGAATTGGA
AACATACTGTACAAGAAATGACATAGTGAACATGCTAGTTGGAAATAAAATTGATAAGGAAAACCGTGAAGTCGATAGAA
ATGAAGGCTTGAAATTTGCACGCAAGCATTCTATGTTGTTCATAGAGGCAAGTGCAAAAACCTGTGATGGTGTTCAGTGT
GCCTTTGAGGAGCTGGTTGAAAAGATCATCCAGACACCTGGACTGTGGGAAAGTGAGAACCAGAACAAAGGAGTCAAGCT
GTCCCCCAGGGAGGAGAGCCACGGGGGGGAGGAGCCTGTGGCGGTTACTGTTCTGTGCTA

Alignment

ORF - retro_rnor_2744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDEDVLTTLKILIIGESGVGKSSLLLRFTDDTFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQERF
          MDED.LTTLKILIIG.SGVGKSSLLLRFTD.TFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQERF
Retrocopy MDEDELTTLKILIIGKSGVGKSSLLLRFTDNTFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQERF

Parental  RTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKFA
          RTLTPSYYRGAQGVILVYDVTRRDTFVKL.NWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKFA
Retrocopy RTLTPSYYRGAQGVILVYDVTRRDTFVKLYNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKFA

Parental  RKHSMLFIEASAKTCDGVQCAFEELVEKIIQTPGLWESENQNKGVKLSPREESHGG-GACGG-YCSVL
          RKHSMLFIEASAKTCDGVQCAFEELVEKIIQTPGLWESENQNKGVKLSPREESHGG.G...G.YCSVL
Retrocopy RKHSMLFIEASAKTCDGVQCAFEELVEKIIQTPGLWESENQNKGVKLSPREESHGG<GGACGGYCSVL

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	0.07 RPM	43.86 RPM
SRP017611_kidney	0.14 RPM	36.22 RPM
SRP017611_liver	0.07 RPM	27.03 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2744 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2744 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009871	1 retrocopy	retro_btau_1691,
Choloepus hoffmanni	ENSCHOG00000005565	4 retrocopies	retro_chof_2391, retro_chof_256, retro_chof_396, retro_chof_846,
Cavia porcellus	ENSCPOG00000002234	2 retrocopies	retro_cpor_633, retro_cpor_652,
Dipodomys ordii	ENSDORG00000014338	1 retrocopy	retro_dord_419,
Monodelphis domestica	ENSMODG00000008253	1 retrocopy	retro_mdom_146,
Oryctolagus cuniculus	ENSOCUG00000022307	2 retrocopies	retro_ocun_1699, retro_ocun_841,
Otolemur garnettii	ENSOGAG00000028015	2 retrocopies	retro_ogar_2587, retro_ogar_2973,
Rattus norvegicus	ENSRNOG00000018972	2 retrocopies	retro_rnor_2744 , retro_rnor_2962,
Sarcophilus harrisii	ENSSHAG00000007613	1 retrocopy	retro_shar_281,