RetrogeneDB ID: retro_lafr_894

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_45:5424242..5425101(-)
• 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_894
GTGGAGCCCAGTCCCACTGCCATGCAGGAGGGCTGGTTCTTTAAGACCTGCAGCTGTGGCCCGGCCAAGCCTTGTCACTG
CAGGTGGAGCAGCTGCTGCACCATGGCGGCTCGCAGTACCAGGACATCCTCGTCTTCTACAGTAAGAACTACAGCAACGC
GCTAGTGTTAGATGGCATCATCCAGTGCACCAAGAGGGACGAATTCTCCTACCAGGAGATGACTGCCAACCTGCCGCTCT
GCAGCCACTCTAACCCACACAAGGTGCTGATCACTGGGGACAGAGGCGTCCTGTGGAACTGGTGAAGCACTCTTCGGTGG
AGGCCATAGTCCAGTGCAAGATTGGCGAGGATGTCATCCAAGTCCCTATGAAGTTCCTCCCAGGCACGGCTCTTGGCTAC
TCCAGCTCAAAGCTAACCCTCCACGTGGGCGACAGTTTTGAGTTCATAAAACAGAACCAGGATGCCTTCCATTTTATCAT
AACTGACTCCCTCAGACCCCATGGGCCCGCTGAGAGCCTCTTCAAGGAATCCTATTACCAGCTCATGAAGACAGCCCTCA
AGAAGGATGGCATTCTCTGTTGTCAGGGTGAGTGCCAGTGACTGCACCTGGACCTCATCAAGGAGATGTGGCAGTTCTGT
AAGTCACTCTTCCCTGTGATGTCCTATGCCTGCTACACCATCCTGACCTATCCCAGCGGCCAGATTAGCTTTATGCTGTG
CAGCAAGAACCCAAGCACCAACTTCCAGGGGCCAGAGCAGCAGCTGACACAGATGCAGGTGGAACAGAGACAGCTGAAAT
ACTACAACTCAGACACGCACTGGGCAATCTTTGTGCTGCCTGAGTCTACCCACAAGGCC

Alignment

ORF - retro_lafr_894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.04 %
• Parental protein coverage: 95.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VAPGPAAIREGWFRETCS-LWPGQALSLQVEQLLHHQRSQYQDILVFRSKTYGNVLVLDGVIQCTERDEF
          V.P.P.A..EGWF..TCS.LWPGQALSLQVEQLLHH..SQYQDILVF.SK.Y.N.LVLDG.IQCT.RDEF
Retrocopy VEPSPTAMQEGWFFKTCS<LWPGQALSLQVEQLLHHGGSQYQDILVFYSKNYSNALVLDGIIQCTKRDEF

Parental  SYQEMIANLPLCSHPNPRKVLIIGGGDGGVLR-EVVKHPSVEAVVQCEIDEDVIQVSKKFLPGMAIAYSS
          SYQEM.ANLPLCSH.NP.KVLI.G..D.GVL..E.VKH.SVEA.VQC.I.EDVIQV..KFLPG.A..YSS
Retrocopy SYQEMTANLPLCSHSNPHKVLITG--DRGVLW<ELVKHSSVEAIVQCKIGEDVIQVPMKFLPGTALGYSS

Parental  SKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKKDGILCCQGECQWLHLDL
          SKLTLHVGD.FEF.KQNQDAF..IITDS..P.GPAESLFKESYYQLMKTALKKDGILCCQGECQ.LHLDL
Retrocopy SKLTLHVGDSFEFIKQNQDAFHFIITDSLRPHGPAESLFKESYYQLMKTALKKDGILCCQGECQ*LHLDL

Parental  IKEMRQFCKSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFREPVQELTQPQVEQRQLKYYNSDVHRA
          IKEM.QFCKSLFPV..YA..TI.TYPSGQI.FMLCSKNPSTNF..P.Q.LTQ.QVEQRQLKYYNSD.H.A
Retrocopy IKEMWQFCKSLFPVMSYACYTILTYPSGQISFMLCSKNPSTNFQGPEQQLTQMQVEQRQLKYYNSDTHWA

Parental  AFVLPEFARKA
          .FVLPE...KA
Retrocopy IFVLPESTHKA

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_894 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,