RetrogeneDB ID: retro_lafr_892

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_45:18172607..18173189(+)
• Located in intron of: ENSLAFG00000011653

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM7
• Ensembl ID: ENSLAFG00000012444
• Aliases: None
• Description: None

Sequence

>retro_lafr_892
GCAGCTGAAACTGATCACACACTCCTTGTGGGCAACCTTGAAACTAACGTGAAAGAGGAGCGCCTTCTCCAGCTTTTCCA
CCAGCCTGGGCCAATATTAAAAATAAAGATCCCAAAAGATAAGGATGGTAAACGTAAGCGATTTGCATTTATGAATTGCA
AACATGAACAATCTGTTCCTTATACAATGAATCTGCTTAATGGAATCAAACTTTTGGAAGGCCTGTCAAAACTCAGTTTA
GATCAGGAAGTAGCCATGACTCGCAGGATGCCAGTAGGTCATATTCCCAGCATCACCTGGGAATTCAAGCCCTACTCTTA
CTCCCACATCTCTCAGCAGCAGGTCTGAAAGGGCCATGGATAACATGACTCCATCAGCACAGGCAATTCAGAGATCGTTT
TCTTCAGAAAATTTTCAGAGACAAGCAGTGATGAACAATGTTTTCAGACACATACCATACGGTGGGAAATTTGGTTCTCT
ACAGTTGGACCAACCAGGATGTTCCCAACAGTGCAGCCACATAATCATTCTCATAACCAGTCTTCAAGCTCCCAGTGGTG
CCAAGGTACCTCATTATCACAG

Alignment

ORF - retro_lafr_892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.37 %
• Parental protein coverage: 72.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AAEADRTLFVGNLEAKVTEEILFELFHQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNLLNGIK
          AAE.D.TL.VGNLE..V.EE.L..LFHQ.GP..K.KIPKDKDGK.K.FAF.N.KHE.SVPY.MNLLNGIK
Retrocopy AAETDHTLLVGNLETNVKEERLLQLFHQPGPILKIKIPKDKDGKRKRFAFMNCKHEQSVPYTMNLLNGIK

Parental  L-FGRPIKIQFRSGSSHALQDVSMPHSQYH-GGNSSPTATPTS-PSRYERPMDNMIPSAQTIQRSFSSPE
          L.FGRP.K.QFRSGSSH..QD.S...SQ.H..GNSSPT.TPTS..SR.ER.MDNM.PSAQ.IQRSFSS.E
Retrocopy L<FGRPVKTQFRSGSSHDSQDASRSYSQHH<PGNSSPTLTPTSLSSRSERAMDNMTPSAQAIQRSFSS-E

Parental  NFQRQAVMKNVLRHMSCGGKFGSIQLDQPGFS-PTIQPHNHSPNQPSSSQWRQDTSSSQ
          NFQRQAVM.NV.RH...GGKFGS.QLDQPG.S.PT.QPHNHS.NQ.SSSQW.Q.TS.SQ
Retrocopy NFQRQAVMNNVFRHIPYGGKFGSLQLDQPGCS<PTVQPHNHSHNQSSSSQWCQGTSLSQ

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_892 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013514	1 retrocopy	retro_cfam_1021,
Choloepus hoffmanni	ENSCHOG00000012747	1 retrocopy	retro_chof_570,
Homo sapiens	ENSG00000076053	1 retrocopy	retro_hsap_2283,
Gorilla gorilla	ENSGGOG00000009941	1 retrocopy	retro_ggor_1696,
Loxodonta africana	ENSLAFG00000012444	1 retrocopy	retro_lafr_892 ,
Myotis lucifugus	ENSMLUG00000023234	2 retrocopies	retro_mluc_1555, retro_mluc_587,
Monodelphis domestica	ENSMODG00000013918	1 retrocopy	retro_mdom_535,
Mus musculus	ENSMUSG00000042396	1 retrocopy	retro_mmus_2436,
Nomascus leucogenys	ENSNLEG00000007323	1 retrocopy	retro_nleu_409,
Oryctolagus cuniculus	ENSOCUG00000003342	1 retrocopy	retro_ocun_924,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,
Pongo abelii	ENSPPYG00000003894	1 retrocopy	retro_pabe_1669,
Pan troglodytes	ENSPTRG00000004305	1 retrocopy	retro_ptro_1617,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,
Tursiops truncatus	ENSTTRG00000001515	3 retrocopies	retro_ttru_1316, retro_ttru_1441, retro_ttru_478,
Vicugna pacos	ENSVPAG00000006300	1 retrocopy	retro_vpac_311,