RetrogeneDB ID: retro_lafr_841

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:53365277..53366054(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030617
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NDFIP2
• Ensembl ID: ENSLAFG00000000864
• Aliases: None
• Description: None

Sequence

>retro_lafr_841
GGTGCTGAGCTCCGAGAGAACTCACCTGCTCGGAAGCTGGATTCCAAGTCGGGCAAGATGATCTCCGCCAGCTGGGCACT
TGAAGCTACTAGGTGCTTCACAATGAAGAGGGTAATTCGGAATCATCTGCTACAGAGCAACCATCAACTTCAAACCCAAC
CCTACAGACCGTACAGACTGCTCCTTCAACACCAGTGCTTGAAACTGACTCTTCTCCACCTGATGGTGCTGTTACTGTAG
AAGTACCTACTTCACATACAGAAGCTTACAGTGACTTTTATCCTGTTCCACCTCCCTACAGTGTTGCTACCTCTCTTCCT
ACAGAGGACAAAGCTGAGAAAGCCAAAGCTGCTGCAATGGCAGCTGCGGCAGCAGAAATACCTCGAAGAATTCGGGAGGA
AGAACGTTCACCAAGAGGTGGCTTCGGGGATGCCAATCAGCTTAGAGTGGGTAATGATGGCATCTTCATGCTGGTGTTTT
TCATGGCATTTATTTTCAACTGGCTTAGATTTTGTTTAACCTTCTGTATAACCAATACCGTAGCTAGAAGGTATGGTGCT
GTCTGTGGATTTGGCCTTTTATTGATCAAATGGATCCTTATTGTCAGGTTTTCTGATTATTTTACTGGATGTTTCAATGG
GCAGTATTGGCTTTGGTGGATATTTCTTGTACTTGGCCTACTCCTTTTCTTCAGAGGATTTGTTCAATTATCTAAAAGTG
AGAAGAAACATGTCTGAAAGTATGGCAGCTGCTCACAGAACAAGGTATTTCTTCTTA

Alignment

ORF - retro_lafr_841 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.61 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAERLGDSRSRKPDSEPGRM-DLHQPGTGRYQVLHNEEDNSESSAIEQPSTSNPTPQIVQTAPSTPVLEN
          GAE....S..RK.DS..G.M.DL.Q.GT..Y.VLHNEE.NSESSA.EQPSTSNPT.Q.VQTAPSTPVLE.
Retrocopy GAELRENSPARKLDSKSGKM<DLRQLGT*SY*VLHNEEGNSESSATEQPSTSNPTLQTVQTAPSTPVLET

Parental  DSSPPPYSSITVEVPTTSDTEAYSEFYPVPPPYSVATSLPTYDEAEKAKAAAMAAAAAETSQRIQEEECP
          DSSPP.....TVEVPT.S.TEAYS.FYPVPPPYSVATSLPT.D.AEKAKAAAMAAAAAE...RI.EEE..
Retrocopy DSSPPD-GAVTVEVPT-SHTEAYSDFYPVPPPYSVATSLPTEDKAEKAKAAAMAAAAAEIPRRIREEERS

Parental  PRDDFSDADQLRVGNDGIFMLAFFMAFIFNWLGFCLSFCITNTIAGRYGAICGFGLSLIKWILIVRFSDY
          PR..F.DA.QLRVGNDGIFML.FFMAFIFNWL.FCL.FCITNT.A.RYGA.CGFGL.LIKWILIVRFSDY
Retrocopy PRGGFGDANQLRVGNDGIFMLVFFMAFIFNWLRFCLTFCITNTVARRYGAVCGFGLLLIKWILIVRFSDY

Parental  FTGYFNGQYWLWWIFLVLGLLLFFRGFV-NYLKV-RNMSESMAAAHRTRYFFL
          FTG.FNGQYWLWWIFLVLGLLLFFRGFV.NYLKV.RNMSESMAAAHRTRYFFL
Retrocopy FTGCFNGQYWLWWIFLVLGLLLFFRGFV>NYLKVRRNMSESMAAAHRTRYFFL

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_841 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021282	2 retrocopies	retro_cjac_2643, retro_cjac_2644,
Cavia porcellus	ENSCPOG00000014687	1 retrocopy	retro_cpor_753,
Loxodonta africana	ENSLAFG00000000864	1 retrocopy	retro_lafr_841 ,
Monodelphis domestica	ENSMODG00000001586	2 retrocopies	retro_mdom_1600, retro_mdom_48,
Mustela putorius furo	ENSMPUG00000003366	1 retrocopy	retro_mputfur_1079,
Tupaia belangeri	ENSTBEG00000005780	1 retrocopy	retro_tbel_3231,