RetrogeneDB ID: retro_lafr_534

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:63351103..63351725(-)
• Located in intron of: ENSLAFG00000000333

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSLAFG00000015364
• Aliases: None
• Description: None

Sequence

>retro_lafr_534
CTAACCGACTACAAAGCCATTATCAAAATCCCAGGCCCTTGGAAGCAAGGCCTAGTCTATCCAACTTACATGTCATTCCG
TCGGGTAGATAAGCCCTCTGAGATAATAGATGTTGGAGACAAAGTGTGTGAGAAGTTTACTAAGAAAGAGAAAAAAATTC
TAGGATAAAAGTATCCATCTACATTGAAATTGTCAACTGAGGGACTGGGGAAGACCTCAATCCCAACAGCATTATTAGTG
TGCAAGAAAAGAGGTGGAGGAGGTCTTTCCAAGATTTTACTAGGGAGAAGATGACCCTCGAAGCTGTCCTGGCACTATCT
CCAAAACGTGAGCGTGCAAAGGTCACTCTGCAAAGGATTGTTTCATGCAACCAGGTGAGACCAAATAGTCTTTGACACCT
GATGAGGAAGAGAAGAAGGAAGAGGCAAATCAGCACAGTTTAATAAGCCTGACCACACAGGGAATTCTTCTAGAAAAAGA
TAGGAAAAAATAAAAAAAGAAACATAAGGATAGAAAGTAATCTGACTCTGACAGTTTAGGTTCAAAAAGTCATACAGTCA
AAAGGGCGAGGCACACATCCAAAGACAGCAAGGCAACAAAGAACAAGCACAAGCAGCACAAG

Alignment

ORF - retro_lafr_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.88 %
• Parental protein coverage: 86.89 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREM-KNDRMKVSLSMKVVNQGT
          .TDY.A.IKIPG..KQGLV..T.MS..RVDKPSEI.DVGDKV..K....E..KN.R.KVS.....VN.GT
Retrocopy LTDYKAIIKIPGPWKQGLVYPTYMSFRRVDKPSEIIDVGDKVCEKFTKKEK<KNSRIKVSIYIEIVN*GT

Parental  GKDLDPNNVIIEQEERRRRSFQDYTGQKITLEAVL-NTTCKKCGCKGHFAKDCFMQPGGTKYSLIPDEEE
          G.DL.PN..I..QE.R.RRSFQD.T..K.TLEAVL..T..K...CKGH.AKDCFMQPG.TK.SL.PDEEE
Retrocopy GEDLNPNSIISVQEKRWRRSFQDFTREKMTLEAVL<GTISKT*ACKGHSAKDCFMQPGETK*SLTPDEEE

Parental  EKEEAKSAAKSAEFEKPDPTKNSRKRKKEKKKKKHRDRKSSDSDSSDSESETGKRARHTSKDSKAAKKKK
          .KEEA..................RK..K.K....H.DRK.SDSDS..S.S.T.KRARHTSKDSKA.K.K.
Retrocopy KKEEANQHSLISLTTQGILLEKDRKK*KKK----HKDRK*SDSDSLGSKSHTVKRARHTSKDSKATKNKH

Parental  KKKK
          K..K
Retrocopy KQHK

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_534 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218,
Dasypus novemcinctus	ENSDNOG00000000509	1 retrocopy	retro_dnov_2548,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534 ,
Myotis lucifugus	ENSMLUG00000000594	1 retrocopy	retro_mluc_2176,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mustela putorius furo	ENSMPUG00000015442	1 retrocopy	retro_mputfur_680,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Sorex araneus	ENSSARG00000007944	1 retrocopy	retro_sara_691,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,