RetrogeneDB ID: retro_lafr_946

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:92469481..92470300(-)
• Located in intron of: ENSLAFG00000013553

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF128
• Ensembl ID: ENSLAFG00000002816
• Aliases: None
• Description: None

Sequence

>retro_lafr_946
ACTTGGCTTGCCCTTATTGAACGGGGAGGTTGTACGTTCACACAGAAAATTAAGGTGGCAGCTGAGAAAGGAGCCAGTGG
TGTGATCATCTATAACTTTCCAGGAACTGGCAATCAGGTTTTTCCCATGTCTCATCAGGCCTTTGAAGACATCGTGGTGG
TGATGATTGGCAACTTGAAAGGCACAGAAATTCTCCATTTAATCCAGAAGGGAATTCACGTCACAGCTGTGGTTGAAGTC
GGGCGGAAACACATCATCTGGATGAACCACTATTTTGTGTCTTTTGTTATTGTTACCACTGCAACCTTAGCCTACTTCAT
CTTTTATCACATTCGAAGACTTTGGGTAGCAAGGATTCAGAACAGGAGATGGCAGCAATTAACAACAGATCTCAATAAGG
CATTTAGCCAGCTGCAACTCCGGGTGTTAAAAGAGGGGGACGAGGAAATCACTCCAAATGGAGACAGCTGTGTAGTTTGC
TTTGAACTCTATAAGCCTAATGATACAGTTCGTGTTCTGACTTGTAAACATTTTTTCCACAAGAATTGCATTGACCCTTG
GATTCTAGCCCATGGGACATGCCCCATGTGCAAATGTGACATCCTTAAAGCTCTGGGGATTCAAGTAGATGTTGAAGATG
GAGCAGAATCATTGCAAGTTCTGATGTCGAACGAATTGCCTGGTACCCTATCACCTATTGATCAGGGGGCGAATAGCGAA
CTTCCTCCTGCAAGATTATCCGATAAAGTGACCCACGTGGATGAGCAGCCTAGGTCTGAGAATGACAGCCAGCCTAATTC
AGTAGTAGAAGAGGTTCAT

Alignment

ORF - retro_lafr_946 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.91 %
• Parental protein coverage: 64.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
          .WLALI.RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PMSH....DIV..MIGNLKGT.IL..IQ
Retrocopy TWLALIERGG-CTFTQKIKVAAEKGASGVIIYNFPGTGNQVFPMSHQAFEDIVVVMIGNLKGTEILHLIQ

Parental  KGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
          KGI.VT.V.EVG.KH..W.NHY...FV.V.....TA...........RRL..AR.Q.R...QL..D..KA
Retrocopy KGIHVTAVVEVGRKHIIWMNHYFVSFVIVT----TATLAYFIFYH-IRRLWVARIQNRRWQQLTTDLNKA

Parental  IGRLQLRTLKQGDEEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
          ...LQLR.LK.GDEEI.P.GDSC.VC.ELYKPND.VR.LTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
Retrocopy FSQLQLRVLKEGDEEITPNGDSCVVCFELYKPNDTVRVLTCKHFFHKNCIDPWILAHGTCPMCKCDILKA

Parental  LGIEVDVEDGSVSLQVPVSSETSNSTSPHEEDNRSETASSGYA-SVQGADEPPLEEHVQSANENLQLVN
          LGI.VDVEDG..SLQV..S.E.....SP......SE.........V...DE.P..E.....N.....V.
Retrocopy LGIQVDVEDGAESLQVLMSNELPGTLSPIDQGANSELPPARLSDKVTHVDEQPRSENDSQPNSVVEEVH

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_946 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946 ,
Loxodonta africana	ENSLAFG00000008735	3 retrocopies	retro_lafr_628, retro_lafr_876, retro_lafr_969,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,