RetrogeneDB ID: retro_lafr_37

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_108:1256154..1257360(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000027388
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NKAP
• Ensembl ID: ENSLAFG00000002962
• Aliases: None
• Description: None

Sequence

>retro_lafr_37
ATGGTGCCTGTGTTCCGGTCCCGCTACCTTGAGGACTCCCAGGCCTCTCGGAGACGGAGACGCAGCTCGTCGGGGAGCCA
GCCATCGGCGCAGGCCAGACGCCCCCCTCGGTGCGGACGCTCCCGGTCTCAGTCCCGGGACCGTGAGGGCTTAAGGCCTC
CGTGGGGTGGGTCGGGCGTGGGCGCTCCTTCCACGCTTAGACCCTCTGGGTCCCGAGAGCGACCCCCTGGGCTCAGCAAC
GATGCCTTCACATCCTCCCCTTCTAGCTATTATGGCGGATATCGCTACCATCATCATCACCATGCTGGTGACTGGCAGGG
GGCCGAAGACTACAAGGAGGAGAGCCATCGGCAGAGGAGGCTGAAAGAGAGAGAGAGGATTGGGGAGTTGGGAGCACCTG
AGGTATGGGGGCTATCTCCAAAATGCCCCGAGCCGGATTCTGATGAGCACACTCCAGTTGAGGGTGAAGCAAAGACTCAG
GAGAGCAGCAGTTCAGATTCTAGCTGGGAAGAAAAGAAAAGGAAGAAGAAGGCCAGTCGTTCAAAAAACAAGAAAAAAAG
AAAGAAAAACTCATCCAAAAGAAAACATAGTAAGTACTCTGATAATGACAGCAGTTCAGACTCTGACTCTGATTCTAGCT
TTGGTGATGATAAAAAGAGACCCAGAAAAGACAAGAAGAAAGAGAAGAAAAAGAAACACAGAGTCAAGAAAACAAAGAAT
ATGAAGACTAAAAAAGAATTTAGGGACTCAACCTGTAAGGATTCAGAAGGAGGGTTGCCAGAAGATAGGTGGATTGAGCA
GCCAAAGACTGCAGATACCATGGGTTTAATAGGCCCAGAAGCACCTATGATATACTACTCTCAAGATGAGAAACCTTTGA
ACTACGGCCATGCGCTGCTTCCAGGTGAAGGTGCAGCTATGGCTGAGTATGTAAAAGCTGGAAAGCGTATCCCACGAAGA
GGTGAAATCGGGCTGACAAGTGAAGAGATTGCTTCATTTGAATGCTCGGGTTATGTCATGAGTGGTAGCAGGCATCGCAG
GATGGAGGCTGTACGACTGCGGAAAGAGAACCAAATCTACAGTGCTGATGAGAAGAGAGCCCTTGCATCCTTTAACCAAG
AAGAAAGACAAAAGAGAGAGAATAAGATTCTAGCCAGTTTCCGAGAGATGGTGTACCGAAAGATAAAAGGGAAAGATGAC
AAATAA

Alignment

ORF - retro_lafr_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPVSGSRTPEREASGSGGKRRSLSRSPKPTRAARSPRSHHSRSHSSSRSGDRNGLSQSSRNQPYRSRSR
          M.PV..SR..E.....S...RRS.S.S.....A.R.PR...SRS.S..R.G.R.....S....P...R..
Retrocopy MVPVFRSRYLE-DSQASRRRRRSSSGSQPSAQARRPPRCGRSRSQSRDREGLRPPWGGSGVGAPSTLRP-

Parental  SRSRERPSGPRGTPFASATSSGYYGGYSRPYGSDKPWPSLLDKEREESLRQKRLSERERIGELGAPEVWG
          S.SRERP.G.....F.S..SS.Y.G...........W....D...EES.RQ.RL.ERERIGELGAPEVWG
Retrocopy SGSRERPPGLSNDAFTSSPSSYYGGYRYHHHHHAGDWQGAEDY-KEESHRQRRLKERERIGELGAPEVWG

Parental  LSPKNPEPDSDEHTPVEDDEPKKSTSSASTSEEEKKKKKKSGRSKERLKKRRKKKSSKRKHKKYSDDSDS
          LSPK.PEPDSDEHTPVE........SS...S.EEKK.KKK..RSK...KK.RKK.SSKRKH.KYSD..DS
Retrocopy LSPKCPEPDSDEHTPVEGEAKTQESSSSDSSWEEKKRKKKASRSKN--KKKRKKNSSKRKHSKYSDN-DS

Parental  DSDSETDSSDEDTKRRAKKNKKKEKKKKHRSKKYKKKKSKKNRKESSDSSSKDSQEEFLENPWKDRSKPE
          .SDS..DSS..D.K.R..K.KKKEKKKKHR.KK.K..K.K...KE..DS..KDS.....E..W....K..
Retrocopy SSDSDSDSSFGDDKKRPRKDKKKEKKKKHRVKKTKNMKTK---KEFRDSTCKDSEGGLPEDRWIEQPKTA

Parental  EPSDLIGPEAPKTLASQDDKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMS
          ....LIGPEAP....SQD.KPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMS
Retrocopy DTMGLIGPEAPMIYYSQDEKPLNYGHALLPGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMS

Parental  GSRHRRMEAVRLRKENQIYSADEKRALASFNQEERRKRENKILASFREMVYRKTKGKDDK
          GSRHRRMEAVRLRKENQIYSADEKRALASFNQEER.KRENKILASFREMVYRK.KGKDDK
Retrocopy GSRHRRMEAVRLRKENQIYSADEKRALASFNQEERQKRENKILASFREMVYRKIKGKDDK

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_37 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 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018433	1 retrocopy	retro_cfam_172,
Dasypus novemcinctus	ENSDNOG00000000072	1 retrocopy	retro_dnov_50,
Echinops telfairi	ENSETEG00000001007	1 retrocopy	retro_etel_1882,
Felis catus	ENSFCAG00000004392	1 retrocopy	retro_fcat_10,
Homo sapiens	ENSG00000101882	1 retrocopy	retro_hsap_15,
Loxodonta africana	ENSLAFG00000002962	1 retrocopy	retro_lafr_37 ,
Macaca mulatta	ENSMMUG00000012382	1 retrocopy	retro_mmul_121,
Mus musculus	ENSMUSG00000016409	1 retrocopy	retro_mmus_279,
Nomascus leucogenys	ENSNLEG00000014922	1 retrocopy	retro_nleu_88,
Otolemur garnettii	ENSOGAG00000001004	1 retrocopy	retro_ogar_239,
Pongo abelii	ENSPPYG00000020679	1 retrocopy	retro_pabe_198,
Pan troglodytes	ENSPTRG00000022233	1 retrocopy	retro_ptro_117,
Rattus norvegicus	ENSRNOG00000031169	1 retrocopy	retro_rnor_93,
Sus scrofa	ENSSSCG00000012613	1 retrocopy	retro_sscr_13,
Ictidomys tridecemlineatus	ENSSTOG00000001134	1 retrocopy	retro_itri_73,