RetrogeneDB ID: retro_lafr_211

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_1:65203750..65204086(-)
• Located in intron of: ENSLAFG00000013806

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND2A
• Ensembl ID: ENSLAFG00000005496
• Aliases: None
• Description: None

Sequence

>retro_lafr_211
TGTAAGGATCATTGTACGTTTGCTGCACATGAGTGTTCCTTTGCATTCAAGAAGGATGTTCAGGTCCTGGTGTGCCCACT
CTGTAACATCCTCATCCCAGTGAAGAAGAGGGAGCTTCCTGGTGTGGTGGTTGGTGAGCTCATGGACCGGGATTGCAAGT
ACAATCCTGGGAGGAGTCACAAGAAGATTTTTACATACCGGTGCTCAAAAGAAGGATGCAAGAAAAAAGAGATGCTGTAG
GTGGTCTATGACAAGTGTCACAGTAACTTCTGCATCAGACACAGACACCCTCTGGACCATGGCTGCAAGTGGGGAGGCTG
CCCCTCCAGCAAAGCC

Alignment

ORF - retro_lafr_211 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 63.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CKDHFTFAAHGCPFAFKKDVQVPVCPLCNSPVPVKKGELPDVVVGEHMDRDCKYNPGRSHEKIFTYRCSK
          CKDH.TFAAH.C.FAFKKDVQV.VCPLCN...PVKK.ELP.VVVGE.MDRDCKYNPGRSH.KIFTYRCSK
Retrocopy CKDHCTFAAHECSFAFKKDVQVLVCPLCNILIPVKKRELPGVVVGELMDRDCKYNPGRSHKKIFTYRCSK

Parental  EGCKRKEMLQVVCDECHSNFCIRHRHPLDHSCKQGGCPPRRA
          EGCK.KEML.VV.D.CHSNFCIRHRHPLDH.CK.GGCP...A
Retrocopy EGCKKKEML*VVYDKCHSNFCIRHRHPLDHGCKWGGCPSSKA

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_211 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015776	1 retrocopy	retro_cjac_2957,
Loxodonta africana	ENSLAFG00000005496	1 retrocopy	retro_lafr_211 ,
Microcebus murinus	ENSMICG00000002112	1 retrocopy	retro_mmur_441,
Monodelphis domestica	ENSMODG00000025494	1 retrocopy	retro_mdom_34,
Sarcophilus harrisii	ENSSHAG00000000364	2 retrocopies	retro_shar_756, retro_shar_779,
Tupaia belangeri	ENSTBEG00000007079	2 retrocopies	retro_tbel_2636, retro_tbel_2697,