RetrogeneDB ID: retro_lafr_971

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_54:14820735..14821586(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000011052
• Aliases: None
• Description: None

Sequence

>retro_lafr_971
ATGGCGGGAGGCCAGGGTGCAGTGACTCGGGGGGCAGGTACGCCTTTCTCGCCAGGATCTCGCCACTTTGGATGTTACCG
GGTTGACACCACTTTACAGGAAGTCATCAGTAGACAAGGCACAATTAATGTAGGTACAATTGATCAGGTAGCTCATGGGA
AACCTCCAGTAGTAAAGGCTATTTCTGGAGTTTACACTGTCAGTTTCAAAAATGAACGAGAAAGAAGTATTAGAGCCATG
CTTGGACGTTTTACTGCTAAGATTTATAAATTTGATGATCTAAGTTGTCTTCGCCCGGAATATTATAGACCCTGTGGAAG
TAGTACGTCGGATGAGTTTCCTACAGACATTCCAGGGACCAAAGGGAACTTAAAATTAGTCAGACATATTTCTTTTGTTG
ACTGTCCTGCCACGATGTTTTGATGGTTACTATGCTGAATGGTCTGGCAGCGATGGATGCAGCTCTCTGTTGATAGCTAG
AAATGAATCTTGTTCTCAGCCTCAGACTTCTGAACACCTGGCTGCTATAGAAATGATGAAACTGAAGCATATTTTGATTC
TACAAAATAATTTGATTTGGTAAAAGAAAGTCAGGCTAAAGAACAGTATGAACAGATCCTTGAGTTTGTACAAGGTGCGG
CAGCCCAAGGAGCTCCTATTACTCCAGTTTCTGCTCAGCTGAAGTAGAATGTTGAAGTTGTCTATGAGTAACAGTGAAAG
GAATGCTGCTACCTCCAAGAGATTTTACTTCAGAACCCCGACTTATTGTTATTAGGTCCTCTGATGTCAACGAGCCTGAC
TGTGAGGTTGATGACCTTAAGGAGGGTGTTTCTGGTAGTAGTATTGGTAAA

Alignment

ORF - retro_lafr_971 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.23 %
• Parental protein coverage: 60.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAGGEAGVTLG-QSHLSSQDLATLDVAKLTPLSH-EVISRQATINIGTIGHVAHGKSTVVKAISGVHTVR
          MAGG...VT.G.Q..LS.QDLATLDV..LTPL...EVISRQ.TIN.GTI..VAHGK..VVKAISGV.TV.
Retrocopy MAGGQGAVTRG>QVRLSRQDLATLDVTGLTPLYR<EVISRQGTINVGTIDQVAHGKPPVVKAISGVYTVS

Parental  FKNELERNITIKLGYANAKIYKLDDPSCPRPECYKSCGSNTPDEFPTDIPGTKGNFKLVRHVSFVDCPG-
          FKNE.ER.I...LG...AKIYK.DD.SC.RPE.Y..CGS.T.DEFPTDIPGTKGN.KLVRH.SFVDCP..
Retrocopy FKNERERSIRAMLGRFTAKIYKFDDLSCLRPEYYRPCGSSTSDEFPTDIPGTKGNLKLVRHISFVDCPA<

Parental  HDILMATMLNGAAVMDAAL-LLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKI-DLVKESQAKEQYE
          HD.LM.TMLNG.A.MDAAL.LLIA.NESC.QPQTSEHLAAIE.MKLKHILILQN...DLVKESQAKEQYE
Retrocopy HDVLMVTMLNGLAAMDAAL<LLIARNESCSQPQTSEHLAAIEMMKLKHILILQNNL<DLVKESQAKEQYE

Parental  QILAFVQGTVAEGAPIIPISAQLKYNIEVVCE-YIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDL
          QIL.FVQG..A.GAPI.P.SAQLK.N.EVV.E...VK....PPRDFTSEPRLIVIRS.DVN.P.CEVDDL
Retrocopy QILEFVQGAAAQGAPITPVSAQLK*NVEVVYE<VTVKGMLLPPRDFTSEPRLIVIRSSDVNEPDCEVDDL

Parental  KGGVAGGSILK
          K.GV.G.SI.K
Retrocopy KEGVSGSSIGK

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_971 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 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971 ,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,