RetrogeneDB ID: retro_lafr_209

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:59083555..59084251(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000004542
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF7L
• Ensembl ID: ENSLAFG00000006941
• Aliases: None
• Description: None

Sequence

>retro_lafr_209
ATGAGTAAGAGCAAAGACGACGCTCCTCATGAACTAGAGAGCCAGTTTATCTTACGCCTACCTCCGGAATATGCCTCGAC
TGTGAGGCGGGCAGTACAGTCTGGCCATGTCAACCTGAAAGACAGACTGACAATTGAGTTACACCCTGATGGTCGTCATG
GTATTGTCAGAGTGGACCGCGTTCCGTTGGCCGCAAAATTGGTAGATCTGCCCTGCGTCATGGAAAGCTTGAAAACCATT
GATAAAAAAACCTTCTACAAGACAGCTGATGTCTGTCAGATGCTTGTAGCCACAGTTGATGGTGATCTCTATCCTCCTGT
GGAAGAGCCAGTTGCTGCCGCTGATCCCAAAGCAAGCAAGAAAAAGGATAAAGACAAAGAGAAAAAGTTTGTCTGGAACC
ATGGAATTACCCTGCCTCTGAAAAATGTCCGAAAGAGAAGGTTTAGGAAGACAGCAAAAAAGAAGTATATTGAATCTCCA
GATGTGGAAAAGGAAGTGAAGAGGTTGCTGAGTACAGATGCTGAAGCTGTCAGTACTCGTTGGGAAATAATTGCTGAAGA
TGAGACAAAAGAGACAGAAAATCAGGGCCTTGATATCGCCTCTCCGGGAATGTCTGGCCACAGGCAGGGCCATGACTCAT
TGGAACATGATGAGCTTCGAGAGATATTCAATGACCTCAGCAGCAGCAGTGAAGAT

Alignment

ORF - retro_lafr_209 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.15 %
• Parental protein coverage: 71. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEGQNELPQELENQFILRLPPEHASTVRKMIRSGNIAMKDKLKIDLHSDGRHAVVQVEDVSLNAKLVDL
          MS......P.ELE.QFILRLPPE.ASTVR....SG....KD.L.I.LH.DGRH..V.V..V.L.AKLVDL
Retrocopy MSKSKDDAPHELESQFILRLPPEYASTVRRAVQSGHVNLKDRLTIELHPDGRHGIVRVDRVPLAAKLVDL

Parental  PCVVASLKTLDKKSFYKTADISQMLVCTTDGDLQSSPEQSVSSTDAKDIEADDGKRRKKYNWKHGITPPL
          PCV..SLKT.DKK.FYKTAD..QMLV.T.DGDL....E..V...D.K.....D....KK..W.HGIT.PL
Retrocopy PCVMESLKTIDKKTFYKTADVCQMLVATVDGDLYPPVEEPVAAADPKASKKKDKDKEKKFVWNHGITLPL

Parental  KNVRKRRFRKIKKKKYTESPDVEKEVKRLLCSDAEAVSARWEVIADGETGEIESQGTVPSFEFSSGMTGH
          KNVRKRRFRK..KKKY.ESPDVEKEVKRLL..DAEAVS.RWE.IA..ET.E.E.QG........SG...H
Retrocopy KNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEIIAEDETKETENQGLDIASPGMSG---H

Parental  KRGPFLSEYEVLRELFPDYSNSEED
          ..G....E...LRE.F.D.S.S.ED
Retrocopy RQGHDSLEHDELREIFNDLSSSSED

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_209 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009247	1 retrocopy	retro_amel_6,
Bos taurus	ENSBTAG00000001979	1 retrocopy	retro_btau_107,
Loxodonta africana	ENSLAFG00000006941	1 retrocopy	retro_lafr_209 ,
Mus musculus	ENSMUSG00000009596	1 retrocopy	retro_mmus_72,
Oryctolagus cuniculus	ENSOCUG00000004497	1 retrocopy	retro_ocun_191,
Rattus norvegicus	ENSRNOG00000026315	1 retrocopy	retro_rnor_134,