RetrogeneDB ID: retro_lafr_322

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:19388081..19388640(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLK10
• Ensembl ID: ENSLAFG00000007611
• Aliases: None
• Description: None

Sequence

>retro_lafr_322
GTGCTGGTGGCTCTGAAGTGGCTGCTCATGGCTGCACGTTGCAGGAAGCCTGTTTTCAGTGTCCTTCTGCTTTACCATTT
CCTTTCACCCACCTGTGATTCTGGGCAGCAGAAGCTCCAAGGGGTCAAATACATTCTCCACCCTGACTTCTCCCACCCTG
GCCACTCCAAAACCTCATGTTTATCAAGATGAACAAAATAACTCATGAGACTCAGAATGTCAAGCCCGTCAACATCTCCT
CTCATTGTCCATCTGCTGGGACCACCTGCTTGGTATCTGGCTGGGGGACTACAAGCAGCCCCCAGGTTAACTTTCACAAG
GCCTTCCAGTGCTTGAACATCACTATGCTAAGCGACAACGGGTGCAGGAAGGCCTACCCAGACCAGGTAGATCTTACCAT
GTTCTGTGCCAGACACAAGGTGGAGCGAGGCTCCTGCCAGAGCAACTCCTGGGGTCCCGTGGTCTGCAGTGGCTCTGTAC
AGGGCCTCGCATCCTGGGGAGATTCCTCTGTGACTAGCCCAACAAACCCAGCATCTACACCAACCTCTACCAGTTCACC

Alignment

ORF - retro_lafr_322 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.97 %
• Parental protein coverage: 75.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLIHGNWVITAAHCKKLNLQVFLGKHNLHQT-ESSQEQISVVQTVTHPGYTNATHD-QDIMLLRLAQPAD
          VL....W...AA.C.K....V.L..H.L..T..S.Q.....V....HP......H..Q..M.........
Retrocopy VLVALKWLLMAARCRKPVFSVLLLYHFLSPTCDSGQQKLQGVKYILHPDFSHPGHS<QNLMFIKMNKITH

Parental  LSDLIRPINISSHCPSAGTTCMVSGWGTTSSPQVKFPKALQCLNITVLSDERCRKAYPGQIDRTMFCAGD
          ......P.NISSHCPSAGTTC.VSGWGTTSSPQV.F.KA.QCLNIT.LSD..CRKAYP.Q.D.TMFCA..
Retrocopy ETQNVKPVNISSHCPSAGTTCLVSGWGTTSSPQVNFHKAFQCLNITMLSDNGCRKAYPDQVDLTMFCARH

Parental  KGGRDSCQGDSGGPVVCNGMLQGLVSWGD-FPCGKPSKPGVYTNLCQFT
          K..R.SCQ..S.GPVVC.G..QGL.SWGD.F.C..P.KP..YTNL.QFT
Retrocopy KVERGSCQSNSWGPVVCSGSVQGLASWGD<FLCD*PNKPSIYTNLYQFT

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_322 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000007611	1 retrocopy	retro_lafr_322 ,
Macropus eugenii	ENSMEUG00000014123	1 retrocopy	retro_meug_1950,