RetrogeneDB ID: retro_lafr_201

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:31302810..31303516(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM92A1
• Ensembl ID: ENSLAFG00000003954
• Aliases: None
• Description: None

Sequence

>retro_lafr_201
ATTGCTGGGTCGCCGCCCAGGGTCCTCCTCAGTGCGTGAGGCAAGCTGTTGAGGCGCAGCCAGGGAAAACCGGGACGCTC
AAACCAGACAACTGCAAAATCCTGTCACAAATGTGGGGAAGCATTTTGGAGAGCTATGCCAAATCTTTGCTGCTTATATG
AGTAAAACTGCCCAACTGCGAGACAAAGCAGACCTCCTGGTGAGTGTAATCAAAGTGTATGCCTCTACAGGGACCCCAAA
TTTAAAGCAGGGCCTGAAAAAACTTTGCTGATGAGTTTGCCAAACTTCAGGATTATCGACAAGCAGAGGTTGAGAGACTT
GAAGTCAAAGTAGTTGAACCTCTGAATGCTTGTGGAACTACTGTAAAAACTAAGCAGGATAACCTCAAAGCAACATTAGT
AGCAAGGAAACGAGAAGCTAAGCAGTTAACACAGAAGAAACATGTCAGCAAAACGTGCCTGATCAACATGTTATGTCACA
GGCAGAAACAGAATTACAGAGAGCTACACTGGACACCATCTGAACAACTCATCACCTGGAGGAAACTATTGACAACTTTG
AAAACCAGAAAATAAAGAATGTATTTTTAGAAGTTATCTCTATTGAAATGTTATTTCGCTGCAAAGCTTTAGAGGTCTAC
ACTGCTGCCTACCAAAATATAGAAAAGGTTGATGAGGAAGGAGATTTAGAGGTTCTCCAAAACTCA

Alignment

ORF - retro_lafr_201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.21 %
• Parental protein coverage: 78.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVGSPPGVLCLARGKMLRRSL-ENRDAQTRQLQDAVTNVEKHFGELCQIFAAYVRKTARLRDKADLLVNE
          ..GSPP.VL..A.GK.LRRS..ENRDAQTRQLQ..VTNV.KHFGELCQIFAAY..KTA.LRDKADLLV..
Retrocopy IAGSPPRVLLSA*GKLLRRSQ>ENRDAQTRQLQNPVTNVGKHFGELCQIFAAYMSKTAQLRDKADLLVSV

Parental  INVYASTETPHLKQGL-KNFADEFAKLQDYRQAEVERLEAKVVEPLKAYGTIVKMKRDDLKATLTARNRE
          I.VYAST.TP.LKQGL.KNFADEFAKLQDYRQAEVERLE.KVVEPL.A.GT.VK.K.D.LKATL.AR.RE
Retrocopy IKVYASTGTPNLKQGL>KNFADEFAKLQDYRQAEVERLEVKVVEPLNACGTTVKTKQDNLKATLVARKRE

Parental  AKQLTQL-ERTRQRNPSDRHVISQAETELQRATMDATRTTRHLEETIDNFEKQKIKDIKNIFSEFITIEM
          AKQLTQ..E...Q..P.D.HV.SQAETELQRAT.D...TT.HLEETIDNFE.QKIK...N.F.E.I.IEM
Retrocopy AKQLTQK<ETCQQNVP-DQHVMSQAETELQRATLDTI*TTHHLEETIDNFENQKIK---NVFLEVISIEM

Parental  LFHGKALEVYTAAYQNIQKIDEEEDLEVFRNS
          LF..KALEVYTAAYQNI.K.DEE.DLEV..NS
Retrocopy LFRCKALEVYTAAYQNIEKVDEEGDLEVLQNS

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_201 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 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009105	1 retrocopy	retro_cfam_1072,
Echinops telfairi	ENSETEG00000013003	1 retrocopy	retro_etel_522,
Homo sapiens	ENSG00000188343	1 retrocopy	retro_hsap_1485,
Gorilla gorilla	ENSGGOG00000006452	1 retrocopy	retro_ggor_1137,
Loxodonta africana	ENSLAFG00000003954	1 retrocopy	retro_lafr_201 ,
Microcebus murinus	ENSMICG00000006797	1 retrocopy	retro_mmur_415,
Monodelphis domestica	ENSMODG00000007447	2 retrocopies	retro_mdom_1239, retro_mdom_827,
Mustela putorius furo	ENSMPUG00000009112	1 retrocopy	retro_mputfur_1183,
Nomascus leucogenys	ENSNLEG00000002773	1 retrocopy	retro_nleu_1707,
Otolemur garnettii	ENSOGAG00000002972	1 retrocopy	retro_ogar_654,
Oreochromis niloticus	ENSONIG00000002446	1 retrocopy	retro_onil_57,
Procavia capensis	ENSPCAG00000011171	1 retrocopy	retro_pcap_272,
Pongo abelii	ENSPPYG00000018744	2 retrocopies	retro_pabe_1235, retro_pabe_2497,
Tarsius syrichta	ENSTSYG00000012502	1 retrocopy	retro_tsyr_975,
Tursiops truncatus	ENSTTRG00000012378	1 retrocopy	retro_ttru_45,