RetrogeneDB ID: retro_lafr_401

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_148:690020..690576(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSLAFG00000017340
• Aliases: None
• Description: None

Sequence

>retro_lafr_401
CTCCAGTCTTTCAGACGCTGTAAGAGAATAACAGCTGACTTTTCTCTTTTCTTAAGCATTGTAGGCAGTAAAGAGCTAGG
CATAATAGCGAGAATCCACCCAAGCCAGTCAAACCTGAAGTCGAGACACCTGAGAAGAAAGAACTATCTGAATTGGAACA
CAAATTTCAGGAGCACATCATTCAAGCCCCTAAACCAGTAGAAGCAATAAAAAGACCAAGCCCATATAAGCCAATGACAA
ATTTGGAATTAAAAATATCTGCCTCCCTCAAACGAGCACTTGATAAACAGTCATCGGGGAATGGAGAAGATAAGAAGGAA
GAAGAAAGAGATGAAATTAAGATTGCACCTCATGTAAAAATGGAGGGTATTCAAAGACATATCAGGATCTACAGAGTCTA
GAAGAAATCTGTGTATATCATTCTGGAGTACTTCTTTTCCAAAAAGTGATGAAATACTGGAGTTGTCATAGAAGAAAAAC
TTCTGATTTTACCACACTTTCAGCCCAAGAGGGTTGTACAACCGGGAAACACATGTGGACTAAAAAAGATGCTGGG

Alignment

ORF - retro_lafr_401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 56.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LKGWSCCKRRTTDFSDFLSIVGCT-KGRHSSEKPPEPVKPEVKTTEKKELSELKPKFQEHIIQAPKPVEA
          L.....CKR.T.DFS.FLSIVG.....RH.SE.PP.PVKPEV.T.EKKELSEL..KFQEHIIQAPKPVEA
Retrocopy LQSFRRCKRITADFSLFLSIVGSK<RARHNSENPPKPVKPEVETPEKKELSELEHKFQEHIIQAPKPVEA

Parental  IKRPSPDEPMTNLELKISASLKQALDKLKLSSGNEEDKKEEENDEIKIG-TPCKNGGCSKTYQSLQSLEE
          IKRPSP..PMTNLELKISASLK.ALD..K.SSGN.EDKKEEE.DEIKI..T.CKNGG.SKTYQ.LQSLEE
Retrocopy IKRPSPYKPMTNLELKISASLKRALD--KQSSGNGEDKKEEERDEIKIA<TSCKNGGYSKTYQDLQSLEE

Parental  ICVYHSGVPVFHEGMKYWSCCRRKTSDFNTFLAQEGCTTGKHLWTKKDAG
          ICVYHSGV..F...MKYWSC.RRKTSDF.T..AQEGCTTGKH.WTKKDAG
Retrocopy ICVYHSGVLLFQKVMKYWSCHRRKTSDFTTLSAQEGCTTGKHMWTKKDAG

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_401 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401 ,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024, retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959, retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,