RetrogeneDB ID: retro_rnor_2754

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: AABR06111295.1:1..661(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gxylt1
• Ensembl ID: ENSRNOG00000005234
• Aliases: Gxylt1, Glt8d3
• Description: Glucoside xylosyltransferase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6GX83]

Sequence

>retro_rnor_2754
CTTTTTTTACGACCAGTTGATGATATTTGGTCTTTACTAAAGAAATTTAATTCCACACAAATTGCTGCAATGGCACCAGA
ACATGAGGAACCTCGAATAGGATGGTATAATCGCTTTGCTAGGCATCCATATTATGGAAAAACTGGAGTAAACTCTGGAG
TTATGTTGATGAACATGACTCGAATGAGAAGGAAGTATTTCAAGAATGATATGACAACTGTACGACTACAATGGGGAGAT
ATACTTATGCCATTGCTTAAAAAATACAAACTAAACATCACATGGGGTGATCAAGATCTATTGAATATCGTGTTTTTTCA
TAATCCAGAAAGCCTTTTTGTTTTTCCGTGTCAATGGAATTATCGACCAGATCATTGTATATATGGAAGCAATTGCCAAG
AAGCAGAAGAAGGAGGAATCTTTATTCTTCATGGGAACAGAGGTGTTTACCATGACGATAAGCAACCAGCATTTAGAGCT
GTTTATGAAGCACTGAGAAATTGTTCTTTTGAAGATGATAACATCCGTTCCTTATTAAAACCTTTAGAACTGGAACTACA
AAAAACAGTGCATACATACTGTGGAAAAATTTACAAAATATTTATCAAACAACTAGCAAAAAGTGTAAGAGATCGTTATG
CCAGATCACCAAAGGAAAAG

Alignment

ORF - retro_rnor_2754 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.45 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFLRPVDDIWSLLERFNSTQIAAMAPEHEEPRVGWYNRFARHPYYGRTGVNSGVMLMNMTRMRRKYFKND
          LFLRPVDDIWSLL..FNSTQIAAMAPEHEEPR.GWYNRFARHPYYG.TGVNSGVMLMNMTRMRRKYFKND
Retrocopy LFLRPVDDIWSLLKKFNSTQIAAMAPEHEEPRIGWYNRFARHPYYGKTGVNSGVMLMNMTRMRRKYFKND

Parental  MTTARLQWGDILMPLLKKYKLNITWGDQDLLNIMFYHNPESLFVFPCQWNYRPDHCIYGSNCREAEEEGV
          MTT.RLQWGDILMPLLKKYKLNITWGDQDLLNI.F.HNPESLFVFPCQWNYRPDHCIYGSNC.EAEE.G.
Retrocopy MTTVRLQWGDILMPLLKKYKLNITWGDQDLLNIVFFHNPESLFVFPCQWNYRPDHCIYGSNCQEAEEGGI

Parental  FILHGNRGVYHDDKQPAFRAMYEALRNCSLEDDSVRSLLKPLELELQKTVHTYCGKTYKIFIKQLAKSIR
          FILHGNRGVYHDDKQPAFRA.YEALRNCS.EDD..RSLLKPLELELQKTVHTYCGK.YKIFIKQLAKS.R
Retrocopy FILHGNRGVYHDDKQPAFRAVYEALRNCSFEDDNIRSLLKPLELELQKTVHTYCGKIYKIFIKQLAKSVR

Parental  NRYDTPPKER
          .RY...PKE.
Retrocopy DRYARSPKEK

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	32.71 RPM
SRP017611_kidney	0.00 RPM	36.98 RPM
SRP017611_liver	0.00 RPM	26.76 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2754 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151233	5 retrocopies	retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258, retro_hsap_4267,
Gorilla gorilla	ENSGGOG00000027928	3 retrocopies	retro_ggor_1702, retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica	ENSMODG00000008913	1 retrocopy	retro_mdom_512,
Mus musculus	ENSMUSG00000036197	1 retrocopy	retro_mmus_2325,
Nomascus leucogenys	ENSNLEG00000017947	1 retrocopy	retro_nleu_2700,
Pongo abelii	ENSPPYG00000004419	2 retrocopies	retro_pabe_1849, retro_pabe_1976,
Pan troglodytes	ENSPTRG00000004836	5 retrocopies	retro_ptro_1623, retro_ptro_2832, retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus	ENSRNOG00000005234	1 retrocopy	retro_rnor_2754 ,