RetrogeneDB ID: retro_rnor_1541

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:151088677..151089434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Aldoa
• Ensembl ID: ENSRNOG00000023647
• Aliases: Aldoa, Aldo1, RNALDOG5
• Description: Fructose-bisphosphate aldolase A [Source:UniProtKB/Swiss-Prot;Acc:P05065]

Sequence

>retro_rnor_1541
ATGTCCTACCCATACCCAGCACTGACCCGGGAGCAGAAGGAGCTGGCTGACATCGCTCACCGAATTGTGGCTCCAGGCAA
GGGCATCCTGGCTGCAGACGAGTCCACTGGAAGCATTGCCGAGCGCCTGCAGTCCATTGGCACCGAGAACACCGGGGAGA
ACAGGCGCTTCTACTGCCAACTGCTGCTGACTGCCGATGACCATGTGAATCCCTGCACTAGCGGGGTGATCCTTTTCCAG
GAGACACTGTACCAGAAGGCAGATGATGGTCATCCCTTCCCCCAAGTTATCAAGTCCAAGGGTGGTGTTGTGGGCATTAA
GGTAGATAAGGGTGTAGTGCCCCTGCTGGAACAAATGGCGAGACCACTACTCAAGGGCTGGATGGGCTGTCTGAACGCTG
TGCCCAGTAAAAGAAAGATGGAGCCGACTTTGTCAAGTGGCGCTGTATGCTAAAGATTGGGGAACACACTCTCTCATCCC
TTGCCATCATGGAAAATGCCAATGTTCTGGCCCGTTACTCCAGCATCTGCCAGCACAATGGCATTGTACCCATGTGGAGC
CTGAAATTCTCCCTGATGGGGACCATGACTTGAAGCGCTGCCAGTATGTTACTGAGAAGGTACCGGCAGCTGTCTACAAG
GCTCTGAGTGACCACCATGTCTCTCTAGAAGGCACATTGCTGAAGCCCAACATGGTCACCCCTGGCCATGCTTGCACCCA
GAAATTTTCCAATGAGTATATTGCCATGGCAACCGTC

Alignment

ORF - retro_rnor_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.62 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPHPYPALTPEQKKELADIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRV
          M..PYPALT.EQ.KELADIAHRIVAPGKGILAADESTGSIA.RLQSIGTENT.ENRRFY.QLLLTADD.V
Retrocopy MSYPYPALTREQ-KELADIAHRIVAPGKGILAADESTGSIAERLQSIGTENTGENRRFYCQLLLTADDHV

Parental  NPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPL-AGTNGETTTQGLDGLSERCAQYK
          NPC..GVILF.ETLYQKADDG.PFPQVIKSKGGVVGIKVDKGVVPL.AGTNGETTTQGLDGLSERCAQ.K
Retrocopy NPCTSGVILFQETLYQKADDGHPFPQVIKSKGGVVGIKVDKGVVPL<AGTNGETTTQGLDGLSERCAQ*K

Parental  KDGADFAKWRCVLKIGEHTPSSLAIMENANVLARYASICQQNGIVPI-VEPEILPDGDHDLKRCQYVTEK
          KDGADF.KWRC.LKIGEHT.SSLAIMENANVLARY.SICQ.NGIVP..VEPEILPDGDHDLKRCQYVTEK
Retrocopy KDGADFVKWRCMLKIGEHTLSSLAIMENANVLARYSSICQHNGIVPM<VEPEILPDGDHDLKRCQYVTEK

Parental  VLAAVYKALSDHHVYLEGTLLKPNMVTPGHACTQKFSNEEIAMATV
          V.AAVYKALSDHHV.LEGTLLKPNMVTPGHACTQKFSNE.IAMATV
Retrocopy VPAAVYKALSDHHVSLEGTLLKPNMVTPGHACTQKFSNEYIAMATV

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	0.22 RPM	1073.70 RPM
SRP017611_kidney	0.14 RPM	762.30 RPM
SRP017611_liver	0.00 RPM	36.38 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1541 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541 , retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,