RetrogeneDB ID: retro_lafr_1098

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:63399472..63400326(+)
• Located in intron of: ENSLAFG00000013733

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL5
• Ensembl ID: ENSLAFG00000011916
• Aliases: None
• Description: ribosomal protein L5 [Source:HGNC Symbol;Acc:10360]

Sequence

>retro_lafr_1098
GGGTTTGTTAAAGGTGCCAAGAACAAGGCCAACTTCAAGAGATACCAAGTGAAATGTAGAGGAAGACAAGAGGGTAAAAC
TGATTCCTGTGCACAGAAATGCTTGGTAATCCAGGATCAAAATAAGTACAGCACACCCAAATACAGGATGATAATTCGTG
TAACCAAAAAGAGATATCATTTGCCAGATTGCTAATACCCATATAGAAGGGGATATGACAATCTGCGTACGTAGCTTATG
CTCACGAACTCCCAAAGTATGGTGTGAAAATTGGTCTGACAAGTTATGCTGCAGCATATCGTACCTGCCTGCTGCTGGTC
CACAGTCTTCTCAATAGGTTTGGCATGGACAAGATCAATAAAGGCCAAGTAAAGGTAACTGGAGATGAATACAATGTGGA
AAGCACTAATGGTCAACCTGGTGCCTTCACGTGCTTTCTGGATGCAAGCCTTGCCACAACTGCCACTAGAAATAAAGTTT
TGGGGGCTCTGAAGAGGGCTGTGGATGGAGGCTTATCTATCACTCACAGTACCAAACAATTCCCTGTTTATGATTCAGAA
GGCAAGGAACTCAATGCAGAAGTATGTCGGAAACACATCATGGGTCAGAATGTTGCAGACTTTTTCTGTTACCTACTGGA
AGAAGATGAAGATGCTTACAAGAAACAATTCTCTTAATATATAAAGTACAACATAACTCCAGATATGACGGAAGAAATGT
ATAAGAAAACACATGCTGCTATACAAGAGAATCCAGTTTATGAGAAGGAACCTAAGAAAGATTTTAAAAAGAAGAGGTGG
AATCATCCCAAAATGTCCCTTGCCCAGAAGGAAGACTGAGTAGCACAGAAGAAA

Alignment

ORF - retro_lafr_1098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.87 %
• Parental protein coverage: 95.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVT-NRDIICQIAYARIE
          GFVK..KNKA.FKRYQVK.R.R.EGKTD..A.K.LVIQD.NKY.TPKYRMI.RVT..RDIICQIA...IE
Retrocopy GFVKGAKNKANFKRYQVKCRGRQEGKTDSCAQKCLVIQDQNKYSTPKYRMIIRVT>KRDIICQIANTHIE

Parental  GDMIVCA-AYAHELPK-YGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQ
          GDM..C........PK.YGVK.GLT.YAAAY.T.LLL...LLNRFGMDKI..GQV.VTGDEYNVES..GQ
Retrocopy GDMTICVRSLCSRTPK>YGVKIGLTSYAAAYRTCLLLVHSLLNRFGMDKINKGQVKVTGDEYNVESTNGQ

Parental  PGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYM
          PGAFTC.LDA.LA.T.T.NKV.GALK.AVDGGLSI.HSTK.FP.YDSE.KE.NAEV.RKHIMGQNVAD..
Retrocopy PGAFTCFLDASLATTATRNKVLGALKRAVDGGLSITHSTKQFPVYDSEGKELNAEVCRKHIMGQNVADFF

Parental  RYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKKDVKKKRWNRPKMSLAQKKD
          .YL.EEDEDAYKKQFS.YIK.N.TPDM.EEMYKK.HAAI.ENPVYEK.PKKD.KKKRWN.PKMSLAQK.D
Retrocopy CYLLEEDEDAYKKQFS*YIKYNITPDMTEEMYKKTHAAIQENPVYEKEPKKDFKKKRWNHPKMSLAQKED

Parental  RVAQKK
          .VAQKK
Retrocopy *VAQKK

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_1098 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 13 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020150	4 retrocopies	retro_cfam_1505, retro_cfam_1696, retro_cfam_905, retro_cfam_906,
Felis catus	ENSFCAG00000024680	5 retrocopies	retro_fcat_281, retro_fcat_304, retro_fcat_453, retro_fcat_458, retro_fcat_463,
Loxodonta africana	ENSLAFG00000011916	6 retrocopies	retro_lafr_1025, retro_lafr_1098 , retro_lafr_302, retro_lafr_988, retro_lafr_989, retro_lafr_992,
Macropus eugenii	ENSMEUG00000006361	3 retrocopies	retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus	ENSMLUG00000008956	1 retrocopy	retro_mluc_925,
Monodelphis domestica	ENSMODG00000011635	1 retrocopy	retro_mdom_748,
Nomascus leucogenys	ENSNLEG00000010500	2 retrocopies	retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus	ENSOANG00000004669	1 retrocopy	retro_oana_97,
Procavia capensis	ENSPCAG00000011865	2 retrocopies	retro_pcap_159, retro_pcap_201,
Petromyzon marinus	ENSPMAG00000002040	1 retrocopy	retro_pmar_23,
Pongo abelii	ENSPPYG00000001152	32 retrocopies	retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Sarcophilus harrisii	ENSSHAG00000006417	1 retrocopy	retro_shar_202,
Tarsius syrichta	ENSTSYG00000014038	8 retrocopies	retro_tsyr_1462, retro_tsyr_1548, retro_tsyr_206, retro_tsyr_248, retro_tsyr_670, retro_tsyr_737, retro_tsyr_786, retro_tsyr_952,