RetrogeneDB ID: retro_lafr_292

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:53865524..53866171(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000027995
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GTF2H3
• Ensembl ID: ENSLAFG00000007300
• Aliases: None
• Description: None

Sequence

>retro_lafr_292
GAAGATGAGTTGAGTCTTCTAGTAATCATAGTTGATACCACCCAATTTGGCGGGGGAAAGCAAGCATTAAAAGAATCTCA
GTTTACTTTATCAAAATGCGTAGATGCTGTGATGGTGTTGGGAAATTCCCATTTATTCATGACTTGTTCCCAAAAACTTG
CTGTGATAGCAAGTCACATTCAAGAAAGTCTATTCTTATATCCTGGAAAGAATGGCAAACTGGGAGACCTCTTTGGAGAA
GTCTGCAACCCTCTTTCTGAATTTAATCCCTCAGGAAGTGAAGATAGAAAATATGAGCTGTTAACAGCAGCAACTGACGT
TATTGCTGAAGAGTCTAAAGACCTAATGACCAAGAGTGACATAAAAGGGCAACACATGGAAACTCTGCTGGCAGGGTCCC
TCACCAAAGCCCTCTGCTACATTCCTAGAATGAACAAGGAAGTTAAACATAATCAGGAAATGCAGTCAAGGATTTGGGTG
ACTATGGCTGCAGAAGACAGTGCATTGCAGTATATGAAATTCATGAATGTAATCTTTGCAGCACAGAAACAGAATATTTT
GATTGATGCTTGTGTTTTAGACAATGATTCAGGACTCCTCCAACAGGCTGTGACATCACAGGGGGACAGTACTTGAAGGT
GTCTCAG

Alignment

ORF - retro_lafr_292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.87 %
• Parental protein coverage: 69.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDELNLLVIIVDTNPIWWGKQALKESQFTLSKCIDAVMVLGNSHLFMNRSNKLAVIASHIHESRFLYPGK
          EDEL.LLVIIVDT.....GKQALKESQFTLSKC.DAVMVLGNSHLFM..S.KLAVIASHI.ES.FLYPGK
Retrocopy EDELSLLVIIVDTTQFGGGKQALKESQFTLSKCVDAVMVLGNSHLFMTCSQKLAVIASHIQESLFLYPGK

Parental  NGRLGDFFGEASNPPSEFNPSGSKDGKYELLTAANEVIAEEIKDLMTKSDIKGQHMETLLAGSLAKALCY
          NG.LGD.FGE..NP.SEFNPSGS.D.KYELLTAA..VIAEE.KDLMTKSDIKGQHMETLLAGSL.KALCY
Retrocopy NGKLGDLFGEVCNPLSEFNPSGSEDRKYELLTAATDVIAEESKDLMTKSDIKGQHMETLLAGSLTKALCY

Parental  IHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNVIFAAQKQSILIDACVLDSDSGLLQQA-CDITGG
          I.RMNKEVK.NQEM.SRI.V..AAEDSALQYM.FMNVIFAAQKQ.ILIDACVLD.DSGLLQQA.CDITGG
Retrocopy IPRMNKEVKHNQEMQSRIWVTMAAEDSALQYMKFMNVIFAAQKQNILIDACVLDNDSGLLQQA<CDITGG

Parental  LYLKVPQ
          .YLKV.Q
Retrocopy QYLKVSQ

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_292 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006219	2 retrocopies	retro_chof_1726, retro_chof_2064,
Loxodonta africana	ENSLAFG00000007300	1 retrocopy	retro_lafr_292 ,
Macropus eugenii	ENSMEUG00000013734	1 retrocopy	retro_meug_558,
Myotis lucifugus	ENSMLUG00000004319	1 retrocopy	retro_mluc_183,
Monodelphis domestica	ENSMODG00000023728	1 retrocopy	retro_mdom_1915,
Tupaia belangeri	ENSTBEG00000011048	8 retrocopies	retro_tbel_1645, retro_tbel_1820, retro_tbel_2555, retro_tbel_3550, retro_tbel_3894, retro_tbel_3931, retro_tbel_4065, retro_tbel_4293,
Tarsius syrichta	ENSTSYG00000007444	1 retrocopy	retro_tsyr_1126,
Tursiops truncatus	ENSTTRG00000007259	1 retrocopy	retro_ttru_1357,