RetrogeneDB ID: retro_lafr_49

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:27404090..27404606(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000029278
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSLAFG00000002502
• Aliases: None
• Description: None

Sequence

>retro_lafr_49
ATGAGCAGTAAGGAATGCTTCAAGTGTGCACACTCTGGCCGTTGGGCTCCGGGATGCCATAAAGGAGGGGGAGCTCGAGG
GCGCAGAGGTAGAGGCCGTGGCAGAGGTTATCCGTGCGGTTCCACCACCCTACCTGACATCTGCTCCCGCTGTGGTGAGT
CCGGTCATCATGCTAAGAACTGTGACCTTCTCGAGGACATCTGCTACAACTGTGGGAGAAGTGGCCACATGGCCAAAGGT
TGTATCGAGCCTAAGCGCGAGAGAGAACAGTGCTGTTACACGTGCGGCAGACCAGGCCATCTGGCTCGTGATTATGACCC
TTTGGCAGAGCAGAAGTGCTACTCTTGCCGCAAATATGCGCACATTCAGAAAGACTGCACCCAAGCCAAGTGCTATCGGT
GCGGTGAGACCAGCCATATGGCCATCAACTGCAGCAACACAAGCGAGGTCAACTGCTACTGCTGTGGCGAGTCCGGTCAT
CTAGCCCGGGAATGCCTCATTGACACTATTGCTTAA

Alignment

ORF - retro_lafr_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQ
          MSS.ECFKC....H..R..P...G...G...RGR.G....RG....S..LPDIC.RCGESGH.AK.CDL.
Retrocopy MSSKECFKCA---HSGRWAP---GCHKGGGARGRRGRGRGRGYPCGSTTLPDICSRCGESGHHAKNCDLL

Parental  EDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYRC
          ED.CYNCGR.GH.AK.C.EPKREREQCCY.CG.PGHLARD.D...EQKCYSC....HIQKDCT..KCYRC
Retrocopy EDICYNCGRSGHMAKGCIEPKREREQCCYTCGRPGHLARDYDPLAEQKCYSCRKYAHIQKDCTQAKCYRC

Parental  GETGHVAINCSKTSEVNCYRCGESGHLARECTIEATA
          GET.H.AINCS.TSEVNCY.CGESGHLAREC.I...A
Retrocopy GETSHMAINCSNTSEVNCYCCGESGHLARECLIDTIA

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_49 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49 ,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626, retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666,