RetrogeneDB ID: retro_lafr_297

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_112:727949..728767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7A
• Ensembl ID: ENSLAFG00000004634
• Aliases: None
• Description: None

Sequence

>retro_lafr_297
ATGAGTGGGGAGGTGACAGGGCAGAACCAGGAGCAGTTTCTGCTTCTGGCCAAGTTGGCCAAGGGGGCAGCACTGGCCAC
ACTCATCCACCAGGTGCTGGAGGCCCCTGGTGTCTACGTCTTTGGGGATCTGCTGGATATACCAAATGTTAGAAAGCTGG
CCAAGAGTGACTTTGCTTCCACATTTCGGCTGCTTACGGTGTTTGCTCATGGGACATATGCTGACTATCTAGCAGAAGCC
CGAAATCTTCCCCCACTCAAAGAGGCCCGGAAGAATAAACTTCGACACCTACCAGTTGTCACGCTGGCCGCCAAAGTCAA
GTGCACCCATATGCAGTGTTGCTGGAAGCCGTTGCCCTGCGTGACGTGCGGCAGTTAGAAGACCTGGTGATTGAGGCTGT
GTATGCCTACGTGCTTCCTGGCTCCCTGGACCAGCGCAATCAGCGGCTGGAGGTTGACTACAGCATTGGGCAGGACATCC
ATCGCCAAGACCTAAGTGCCATTGTCCGAACCCTTTAGGAGTGGTGTGTGGGCTGTGAGGTTGTGCTGTCAGGCATCAAG
GAGAAAGTAAGCCAGGCCAACCAGCACAAGGAGGAGCAGCTGGGCCTAAAGCAGCAGATCGAGAGTGAGGTTGCCAACCT
TAAGAAAACCGTTAAAGTTACAATGGCAGCCACAGCTACAGCCACATCTCAGGACCCTGAGCAACACCTGACTGAGCTGA
AGGAACCAGCTCCTGGCATCAACCAGCGCCAGCCCAGCAAGAAAACCTCAAAGGGCAAGGGGCTCTGAGGGAGCTCCAAG
GTTTGGTCCAAGTTGAAC

Alignment

ORF - retro_lafr_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSGEVKVTGQNQEQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVF
          MSGEV..TGQNQEQFLLLAK.AKGAALATLIHQVLEAPGVYVFG.LLD.PNVR.LA.SDFASTFRLLTVF
Retrocopy MSGEV--TGQNQEQFLLLAKLAKGAALATLIHQVLEAPGVYVFGDLLDIPNVRKLAKSDFASTFRLLTVF

Parental  AYGTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCI-PYAVLLEALALRNVRQLEDLVIEAVYAD
          A.GTYADYLAEARNLPPL.EA.KNKLRHL.VVTLAAKVKC..PYAVLLEA.ALR.VRQLEDLVIEAVYA.
Retrocopy AHGTYADYLAEARNLPPLKEARKNKLRHLPVVTLAAKVKCT<PYAVLLEAVALRDVRQLEDLVIEAVYAY

Parental  VLRGSLDQRNQRLEVDYSIGRDIQRRDLSAIARTLQEWCVGCEVVLSGIEEQVSRANQHKEQQLGLKQQI
          VL.GSLDQRNQRLEVDYSIG.DI.R.DLSAI.RTL.EWCVGCEVVLSGI.E.VS.ANQHKE.QLGLKQQI
Retrocopy VLPGSLDQRNQRLEVDYSIGQDIHRQDLSAIVRTL*EWCVGCEVVLSGIKEKVSQANQHKEEQLGLKQQI

Parental  ESEVANLKKTIKVTTAAAAAATSQDPEQHLTELREPAPGTNQRQPSKKTSKGKGLRGSAKIWSKSN
          ESEVANLKKT.KVT.AA.A.ATSQDPEQHLTEL.EPAPG.NQRQPSKKTSKGKGL.GS.K.WSK.N
Retrocopy ESEVANLKKTVKVTMAATATATSQDPEQHLTELKEPAPGINQRQPSKKTSKGKGL*GSSKVWSKLN

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_297 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000004634	1 retrocopy	retro_lafr_297 ,
Macropus eugenii	ENSMEUG00000010451	1 retrocopy	retro_meug_724,
Microcebus murinus	ENSMICG00000013661	1 retrocopy	retro_mmur_1458,
Oryctolagus cuniculus	ENSOCUG00000011187	1 retrocopy	retro_ocun_1086,
Ictidomys tridecemlineatus	ENSSTOG00000027250	1 retrocopy	retro_itri_538,