RetrogeneDB ID: retro_lafr_408

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:37044737..37045120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSLAFG00000003811
• Aliases: None
• Description: None

Sequence

>retro_lafr_408
ATGGCTGAGGAGCTCTCTATGACCACATCTTACCCCGTAGGTGATTTCTGCTGCCCCGTCTGTCGGGGGTGCTCAAAACA
CCTGTCCCTACTGCGGCTGGTCATCACGTTTTCTACAGAGAATATTTCCTGACTGCAATGAGAGAAAGCAGAATACATTG
TCCCCTCTCTCGTGGAATTATGACTAGAAGAAAGACAGCATGTCCTGAATGAGATTTAGTCCTTGAAAATACCATGAGGA
AGTTTTCTGGTAGCTGCAGATACTGTGAAAACCAGATTAAATTCTATCACATGAGACAACATTGCAAATTTTGGAAGAAG
TTTCCAGATGAATATGATGTTTTTTGTACCATTCCAAACTTTCAGATTTCTCAAGCTTCGGTT

Alignment

ORF - retro_lafr_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.44 %
• Parental protein coverage: 52.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEELSAATSYTEDDFYCPVCQE-VLKTPVRTAACQHVFCRKCFLTAMREGGVHCPLCRGNVTRRERACP
          MAEELS..TSY...DF.CPVC...VLKTPV.TAA..HVF.R..FLTAMRE...HCPL.RG..TRR..ACP
Retrocopy MAEELSMTTSYPVGDFCCPVCRG<VLKTPVPTAAGHHVFYREYFLTAMRESRIHCPLSRGIMTRRKTACP

Parental  ERALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVSSIIPNFQISQDSV
          E..L.LEN.MRKFSGSCR.C..QIKFY.MR.H.K..KK..DEY.V...IPNFQISQ.SV
Retrocopy E*DLVLENTMRKFSGSCRYCENQIKFYHMRQHCKFWKKFPDEYDVFCTIPNFQISQASV

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_408 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408 ,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,