RetrogeneDB ID: retro_lafr_273

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:21314556..21314972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000009621
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GOLGA7
• Ensembl ID: ENSLAFG00000009146
• Aliases: None
• Description: None

Sequence

>retro_lafr_273
GCGGCCCATCCTGTCCTCCCCATGAGGCCGCAGCAAGGGCGGATGTCCGCCAGTGTCGGGGAAGGTCTTCATTCAGCGAG
ACTACAGCAGTTCCAGACCAAGCTCACCGCAGAGCTGGAGAACCAGATTGATAGACAACAATTTGAAAAAATAATTAGAA
TTTTAAATAAAGTTTATGCAGAAGCAGAGAAGCTTGGAGGCCAATCATATCTTGAAGGCTGTTGGCTTGTATAGCAGCAT
ACATCATCTTTTTATGCATGGAAACTGATTATGAGAAGGTTCTAAAGAAAGCCTCCAAGTATTTTCAAAAGCAGAGTGAG
AACATACATGCTCCCCAAGGCCTCCTTCTGACAGATCCCATTGAGAAACGACTTCGAGTTATTGAACTTACCATATATGG
AGACAGAGGCGTGAGC

Alignment

ORF - retro_lafr_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.72 %
• Parental protein coverage: 97.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAHPVLAMRPQQAPVSGKVFIQRDYSSGTRCQFQTKFPAELENRIDRQQFEETVRTLNNLYAEAEKLGGQ
          AAHPVL.MRPQQ...S..........S....QFQTK..AELEN.IDRQQFE...R.LN..YAEAEKLGGQ
Retrocopy AAHPVLPMRPQQGRMSAS--VGEGLHSARLQQFQTKLTAELENQIDRQQFEKIIRILNKVYAEAEKLGGQ

Parental  SYLEGC-LACLTAYTIFLCMETHYEKVLKKVSKYIQEQNEKIYAPQGLLLTDPIERGLRVIEITIYEDRG
          SYLEGC.LAC..AY.IFLCMET.YEKVLKK.SKY.Q.Q.E.I.APQGLLLTDPIE..LRVIE.TIY.DRG
Retrocopy SYLEGC<LACIAAYIIFLCMETDYEKVLKKASKYFQKQSENIHAPQGLLLTDPIEKRLRVIELTIYGDRG

Parental  MS
          .S
Retrocopy VS

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_273 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 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002741	1 retrocopy	retro_amel_1785,
Dasypus novemcinctus	ENSDNOG00000009976	2 retrocopies	retro_dnov_194, retro_dnov_45,
Erinaceus europaeus	ENSEEUG00000013699	1 retrocopy	retro_eeur_588,
Felis catus	ENSFCAG00000018740	3 retrocopies	retro_fcat_1209, retro_fcat_1958, retro_fcat_975,
Homo sapiens	ENSG00000147533	1 retrocopy	retro_hsap_3862,
Loxodonta africana	ENSLAFG00000009146	1 retrocopy	retro_lafr_273 ,
Microcebus murinus	ENSMICG00000000940	1 retrocopy	retro_mmur_721,
Myotis lucifugus	ENSMLUG00000014516	2 retrocopies	retro_mluc_1348, retro_mluc_787,
Monodelphis domestica	ENSMODG00000010474	2 retrocopies	retro_mdom_1034, retro_mdom_1528,
Mus musculus	ENSMUSG00000015341	3 retrocopies	retro_mmus_2687, retro_mmus_312, retro_mmus_3572,
Nomascus leucogenys	ENSNLEG00000012577	1 retrocopy	retro_nleu_3014,
Oryctolagus cuniculus	ENSOCUG00000007546	1 retrocopy	retro_ocun_1503,
Otolemur garnettii	ENSOGAG00000003707	2 retrocopies	retro_ogar_2968, retro_ogar_3484,
Pongo abelii	ENSPPYG00000018542	1 retrocopy	retro_pabe_276,
Pan troglodytes	ENSPTRG00000020193	1 retrocopy	retro_ptro_2632,
Rattus norvegicus	ENSRNOG00000017956	1 retrocopy	retro_rnor_2793,
Sarcophilus harrisii	ENSSHAG00000016094	2 retrocopies	retro_shar_123, retro_shar_626,
Ictidomys tridecemlineatus	ENSSTOG00000004024	3 retrocopies	retro_itri_1181, retro_itri_1774, retro_itri_359,
Tarsius syrichta	ENSTSYG00000005197	3 retrocopies	retro_tsyr_1835, retro_tsyr_359, retro_tsyr_714,