RetrogeneDB ID: retro_lafr_945

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:92343441..92344097(-)
• Located in intron of: ENSLAFG00000013553

Retrocopy information

• Ensembl ID: ENSLAFG00000032352
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSLAFG00000002873
• Aliases: None
• Description: None

Sequence

>retro_lafr_945
TGGTCGGGCCTGGCCCTGGGTGTGCAGGGTGTTGTCCTGCGGCTTCCAGGGCTAACCCAAGTGAGATGGAGTTGCTATGG
CCCTGAATACCAGGATCCCCAGACTGATAAGGAATATTACCGCAAGCCCATGGCCAAGCTGACTAAGGAGGAAAAGTATG
AGCAGGAGCTCAGTAAGACTCAGGTCATCAAAAATGCCCCAGCGACCAAAATAAGCTCTGTGTTTGAAGACCCAGTGGTC
AGTAAATTCACCAACATGATGACGAAAGGAGGAAACAAAGTGCTGGCCAGGTTCCTCATGCTACAGACCTTGGAAACTGT
GAAAAGGAAGCAATTTGAGAAGTACCATGCTGCTTCTGCAGAGGACCAGGCAACCACTGAACACAATCCGAACACCATCT
TCCACCAGGCTCTAGAAAACTGTGAGCCTGTGATTGGGCTGGTACCTATTCTCAAGGTCAGCCTCTTCTACCAGGTTTTC
GTGCCCCTATCCAACTGGCATCGCTGCTTCCTGGGCACGAAGTGGATGCTCACTGAGTGCTGGAGGGAAGAAGCACCAGC
AGATGTGATGCCGGAGAAGCAGTCACATGAGCTGCTACAGGCTTTCCACAACCGAGCCTGGTAAACAAGAGGAAACACAA
CATGCACAAGATGGCC

Alignment

ORF - retro_lafr_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.93 %
• Parental protein coverage: 90.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WSGLALGVRGVVLRLPGLTQVRWSRYGPEFQDPQTDKEYYRKPTAQLTEEEKYERELRKTRFIKAAPATK
          WSGLALGV.GVVLRLPGLTQVRWS.YGPE.QDPQTDKEYYRKP.A.LT.EEKYE.EL.KT..IK.APATK
Retrocopy WSGLALGVQGVVLRLPGLTQVRWSCYGPEYQDPQTDKEYYRKPMAKLTKEEKYEQELSKTQVIKNAPATK

Parental  TSSVFEDPVVSKFTNMMMKGGNKVLARHLMTQTLETVKRKQFEKYHAASAKEQATIERNPYTIFHQALKN
          .SSVFEDPVVSKFTNMM.KGGNKVLAR.LM.QTLETVKRKQFEKYHAASA..QAT.E.NP.TIFHQAL.N
Retrocopy ISSVFEDPVVSKFTNMMTKGGNKVLARFLMLQTLETVKRKQFEKYHAASAEDQATTEHNPNTIFHQALEN

Parental  CEPVIGLVSILKSGRFYQVPVPLADRRRRFLAMKWMITECRE-KKHRRM-LMPEKLSHELLQAFHNQ-GP
          CEPVIGLV.ILK...FYQV.VPL....R.FL..KWM.TEC...KKH..M..MPEK.SHELLQAFHN....
Retrocopy CEPVIGLVPILKVSLFYQVFVPLSNWHRCFLGTKWMLTECWR>KKHQQM<VMPEKQSHELLQAFHNR<SL

Parental  VVKRKRDMHKMA
          V.KRK..MHKMA
Retrocopy VNKRKHNMHKMA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_945 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316,
Erinaceus europaeus	ENSEEUG00000015775	1 retrocopy	retro_eeur_212,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013, retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945 ,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Oryctolagus cuniculus	ENSOCUG00000017928	1 retrocopy	retro_ocun_609,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,
Ictidomys tridecemlineatus	ENSSTOG00000015200	2 retrocopies	retro_itri_1805, retro_itri_461,