RetrogeneDB ID: retro_lafr_617

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_25:29808749..29809379(-)
• Located in intron of: ENSLAFG00000012506

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL7A
• Ensembl ID: ENSLAFG00000007425
• Aliases: None
• Description: None

Sequence

>retro_lafr_617
GTCTCAGGTAGGTTGGTTTGAGCCAACACCAGGAGCCGGGCCAAAGATGATATCAAGAGGGTCATGGCAGCTATGGAGAA
AGTGTGCAAATGGGAGAAGAAGTGGGTGCCTGTGGATGATACGTCCCTGTGAATCTACAAGTGGCTCTCTGTGATGGAGT
CCGGGGTTGACAATAAAAACAAAAACAAGTAGAAGGGCAAGGATGAGAAGTGTGGCTCAGAGGTGGCCACTCTGGAGAAC
AGCTCCTATCCGGGGATGATGGACATGCATGATGACAACAGCAACCAGAGCTCCATTGGAGGTGCCTCCCCCATCAAAAG
GGAGAACAGCAGTAACTCCAGCCCTGCTCCAGAGCCCAACTCAGCCGTGCCCAGTGATGATGCAGAAGCCAAGGTGGATG
AAACCCAGGCTGATGGGAAGGAGTACCTCAGGGCCAAAGATGCCTCTGACGAGCAGAACTCGCACTCTTTGATGGAAAAC
TCGACAAGCAGCTCAGAAAAAGTGGAAAGGCAGCCATCTGGTGATACGAGTCTCACCACAGACACATCAGAACTCTCTCA
AGATTTGGAAGGAGTGCCACCCTTGAAAAAGATGAAACTGGAGGCTTACCAACAAAACTCCAAGGAGATG

Alignment

ORF - retro_lafr_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGRSVRAETRSRAKDDIKRVMAAIEKVRKWEKKWVTVGDTSLRIYKWVPVTEPKVDEKNKNKKKGKDEK
          .SGR.V.A.TRSRAKDDIKRVMAA.EKV.KWEKKWV.V.DTSL.IYKW..V.E..VD.KNKNK.KGKDEK
Retrocopy VSGRLV*ANTRSRAKDDIKRVMAAMEKVCKWEKKWVPVDDTSL*IYKWLSVMESGVDNKNKNK*KGKDEK

Parental  CGSEVTTPENSSSPGMMDMHDDNSNQSSIADASPIKQENSSNSSPAPEPNSAVPGDGAEAKVDETQADGK
          CGSEV.T.ENSS.PGMMDMHDDNSNQSSI..ASPIK.ENSSNSSPAPEPNSAVP.D.AEAKVDETQADGK
Retrocopy CGSEVATLENSSYPGMMDMHDDNSNQSSIGGASPIKRENSSNSSPAPEPNSAVPSDDAEAKVDETQADGK

Parental  EHLGAEDASDEQNSQSSMENS-NSSEKVERQPSGDAGLATDTSAISQDLEGVPPSKKMKLEASQQNSEEM
          E.L.A.DASDEQNS.S.MENS..SSEKVERQPSGD..L.TDTS..SQDLEGVPP.KKMKLEA.QQNS.EM
Retrocopy EYLRAKDASDEQNSHSLMENSTSSSEKVERQPSGDTSLTTDTSELSQDLEGVPPLKKMKLEAYQQNSKEM

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_617 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013429	1 retrocopy	retro_dnov_1682,
Loxodonta africana	ENSLAFG00000007425	1 retrocopy	retro_lafr_617 ,
Macropus eugenii	ENSMEUG00000013687	2 retrocopies	retro_meug_1658, retro_meug_611,
Oryctolagus cuniculus	ENSOCUG00000000630	1 retrocopy	retro_ocun_1504,