RetrogeneDB ID: retro_lafr_914

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:7839758..7840456(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSLAFG00000007927
• Aliases: None
• Description: None

Sequence

>retro_lafr_914
GCCAGTCTAATTGAAGCCAATAGAGAACTAAAGATCTTTATAGACCAGAATCATAGTCCTGGAAAAAGTGTGGGATCATT
TGTAGCTGTTCATCCTTCTACTGTAAATATACTTGGAAAACAACACCTGCCAAAAACTTTTGGACAGTCCAGTGTCAACA
CTGCACAGCAAGTGGTAATTGGTATGCCTCACATACCTTCAGCACCAAATACTATCCTGGTGGGAAGTCCACACACTCCT
AACACACACTTTGTATCTCAGAACCAGGCTTCAGACTCCTCACCTTGGTCTGCTGGCAAATGCAACAGAAAAGGAGAGAA
GAATGGCAAGGGTCTGAGGCATTTTTCAATGAAGTTTTGTGAAGAGGTTCAGAAGAAAGGAACCATTTCATATAATGAAG
TGGCAGATGAGTTGGCTGCAGAGTTCGGTGTTGCAAATAACCATATTTTACCAAATGAATCAGCTTATGACCAGAAGAAT
ATAAGACAATGAGTCTATGATGCCTTAAATGTCTTAATGGCCATGAACATCATCTCTAAGCGGAAGAATTCAAATGGATC
GGTCTGCCTACTAACTTGGCTCAGGAATGTTAGAATTTAGAAGTAGAGAGACAGAGAAGACGTGAAGGAATAAAACAGAA
ACATTCTCAACTTCAAGAACTTTTTCAACAGAAAATTGCCTTGAAGAATCTGGTGCAG

Alignment

ORF - retro_lafr_914 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 57.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGLIEANGELKVFIDQNLSPGKGVVSLVAVHPSTVNTLGKQLLPKTFGQSNVNIAQQVVIGTPQRPAAPN
          A.LIEAN.ELK.FIDQN.SPGK.V.S.VAVHPSTVN.LGKQ.LPKTFGQS.VN.AQQVVIG.P..P.APN
Retrocopy ASLIEANRELKIFIDQNHSPGKSVGSFVAVHPSTVNILGKQHLPKTFGQSSVNTAQQVVIGMPHIPSAPN

Parental  TIVVGSPHTPNTHFVSQNQASDSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKVQRKGTTSYNEVADELVA
          TI.VGSPHTPNTHFVSQNQASDSSPWSAGK.NRKGEKNGKGLRHFSMK.CE.VQ.KGT.SYNEVADEL.A
Retrocopy TILVGSPHTPNTHFVSQNQASDSSPWSAGKCNRKGEKNGKGLRHFSMKFCEEVQKKGTISYNEVADELAA

Parental  EFSAADNHILPNESAYDQKNIRRRVYDALNVLMAMNIISKEKK-EIKWIGLPTNSAQECQNLEVERQRRL
          EF..A.NHILPNESAYDQKNIR..VYDALNVLMAMN.I....K.E.KWIGLPTN.AQEC.NLEVERQRR.
Retrocopy EFGVANNHILPNESAYDQKNIRQ*VYDALNVLMAMN-IISKRK<EFKWIGLPTNLAQEC*NLEVERQRRR

Parental  ERIKQKQSQLQELILQQIAFKNLVQ
          E.IKQK.SQLQEL..Q.IA.KNLVQ
Retrocopy EGIKQKHSQLQELFQQKIALKNLVQ

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_914 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 11 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914 ,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,