RetrogeneDB ID: retro_lafr_1175

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:65255778..65256640(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSLAFG00000028297
• Aliases: None
• Description: None

Sequence

>retro_lafr_1175
CCCGACCCCGACGGCCCCACCGCCATCTGTGAGGGCCGGTTGCACGAGACCTGCAGCCTGTGGCCGGCCAGGGCTGGTCG
CTGCAGGTGGAGCGGTCGCTGCACCATCAGCGCTCACGATACCAGGACGTCCTGGTCTTCCACAGTAAGACCTACGGCAA
CGTGCTGGTGTTGGACGACATCATCCAGTGCGCTGAGAGAGAGGAGTCCTTCTACCAGGAGATGATTGCCAACTTGCCCC
TCCTCAGCCACCCTAACCTGACAAGACGCTTATGATCGGGGTGGGGACCGAGGCGTCCTGCGGGAAGTGGTAAAGCACTC
GGCAGTGGAGGCCATGGTCCAGAGCGAGATCGATTAGGGTGTCATCCGAGTGTCTAAGAAGTTCCTGCCGGGCATGGCCG
TTGGCTACTCCAGCTCAAAGCTGACCCTCCATGTGGGCGACGGTTTTGAGTTCATGAAATAGAACCAGGATGCCTTCGAT
GTATCATCACTGACTCCTTAGACTCCATGGGCCCCGCCGAGAACCTCTTCAGTAAGTCCTATGGCCAGCTCACGAAGACC
GGCCTCAAGGAAGATGGCATTCTCTGCTGCCAGGGTGAGTGCCAGTGGCTGCACCTGGGCCTCCTCAAGGAGACGCAGTA
GTTCCGTAAGTTACTCTTTCCTGTGGTGGCCTATGCCTACCGCAACATCCCCGCCTACCCCGGCAGCCAGATCCGGCTTT
ATGCTGCGCAGCTGCAAGACCCGAGCGCCAACTTCCGGGAGCCGGTGCAGCAGCTGACGCAGGCGCAGAGGGAGTAGAGC
CCGCTGAAACGCTCAGACGTGCCCCGGCAGCTTTTGCGTTGCCGGAGTTTGCTTGCAAGAGC

Alignment

ORF - retro_lafr_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.28 %
• Parental protein coverage: 96.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PVAPGPAAIREGWFRETCSLWP-GQALSLQVEQLLHHQRSQYQDILVFRSKTYGNVLVLDGVIQCTERDE
          P...GP.AI.EG...ETCSLWP.GQ..SLQVE..LHHQRS.YQD.LVF.SKTYGNVLVLD..IQC.ER.E
Retrocopy PDPDGPTAICEGRLHETCSLWP<GQGWSLQVERSLHHQRSRYQDVLVFHSKTYGNVLVLDDIIQCAEREE

Parental  FSYQEMIANLPLCSHPN-PRKVLIIG-GGDGGVLREVVKHPSVEAVVQCEIDEDVIQVSKKFLPGMAIAY
          ..YQEMIANLPL.SHPN.P.K.L.IG.GGD.GVLREVVKH..VEA.VQ.EID..VI.VSKKFLPGMA..Y
Retrocopy SFYQEMIANLPLLSHPN<PDKTLMIG<GGDRGVLREVVKHSAVEAMVQSEID*GVIRVSKKFLPGMAVGY

Parental  SSSKLTLHVGDGFEFMKQNQDAFDV-IITDSSDPMGPAESLFKESYYQLMKTALKKDGILCCQGECQWLH
          SSSKLTLHVGDGFEFMK.NQDAFDV.IITDS.D.MGPAE.LF..SY.QL.KT.LK.DGILCCQGECQWLH
Retrocopy SSSKLTLHVGDGFEFMK*NQDAFDV<IITDSLDSMGPAENLFSKSYGQLTKTGLKEDGILCCQGECQWLH

Parental  LDLIKEMRQFCKSLFPVVAYAYCTIPTYPSGQIGFMLCS-KNPSTNFREPVQELTQPQVEQRQLKYYNSD
          L.L.KE...F.K.LFPVVAYAY..IP.YP..QI.........PS.NFREPVQ.LTQ.Q.E...LK...SD
Retrocopy LGLLKETQ*FRKLLFPVVAYAYRNIPAYPGSQIRLYAAQLQDPSANFREPVQQLTQAQRE*SPLK--RSD

Parental  VHR-AAFVLPEFARKA
          V.R.AAF.LPEFA.K.
Retrocopy VPR<AAFALPEFACKS

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_1175 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Loxodonta africana	ENSLAFG00000028297	2 retrocopies	retro_lafr_1175 , retro_lafr_894,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Myotis lucifugus	ENSMLUG00000017585	1 retrocopy	retro_mluc_2458,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Ochotona princeps	ENSOPRG00000012079	1 retrocopy	retro_opri_1119,