RetrogeneDB ID: retro_lafr_688

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_30:17517383..17518078(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DRAM2
• Ensembl ID: ENSLAFG00000007736
• Aliases: None
• Description: None

Sequence

>retro_lafr_688
CTCCATCATGTTGACCCTGTTTTTGCCTTCTATCAGTGACAGCGGTAGCTCTAGAAAAATGCTTGTTTGGGGCAGTGTTA
AACATCACTGCAGTTTTATGTGTTGCTACCATTCATGTTTGTTGTAAGCAAGTCCATGCTGTGAACCCTGAAGACAGTCG
TATCATGAGATTAAACAAAGCTGGCCTTGTAGTTGGATTACGGAGTTGCTTAGGACTTTCTATTGTGGCAAACTTCTAGA
AAACAACCCTTTTTCTTGCACGTGTAAGTGGAGCTGTGCTCACCTTTGGTCCGGGCTCGTTACATATGTTTGTTCAGACT
ATCCTTTCCTACCAAATGCAGGCTACAATTCATGGCAAGCAAGTCTTCTGGATCAGACTACTGGTGGTTATCTGGTGTCC
ATTAAGTGCATTTAGCATGCTGACTTGTTCATCTCTTTTGTACAGTGGCAGTTTTGACACCGATATAGCACAGAAACTCC
ATTGGAACCCTGAGGAAGAAGGCTATGTGCTTCACATGATAACTACTGCTGTAGAATGGTCAATGTCATTGGCCTTCATT
GGCTTTTTTCTGACTTATAGTTGTGATTTTCAGAAAATTTCTTGACAGGTGGAAGCCAGTTTACAAGGATTAACTCTCTA
TGACATTGCTGTTTGCCCAGTTAACAATGAACCAACATGACTACTTTCCAGAGAT

Alignment

ORF - retro_lafr_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.91 %
• Parental protein coverage: 87.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHHVDPVLPY-ISDTGTVAPEKCLFGAMLNVTAVLCVATIYVRYKQVHALNPDENRIIRLNKAGLVLGLF
          LHHVDPV.....S.T..VA.EKCLFGA.LN.TAVLCVATI.V..KQVHA.NP...RI.RLNKAGLV.GL.
Retrocopy LHHVDPVFAF<LSVTA-VALEKCLFGAVLNITAVLCVATIHVCCKQVHAVNPEDSRIMRLNKAGLVVGLR

Parental  SCLGLSIVANFQKTTLFLAHVSGAVLTFGLGSLYMFVQTILSYQMQPRIHGKQVFWIRLLVVIWCAVSAF
          SCLGLSIVANF.KTTLFLA.VSGAVLTFG.GSL.MFVQTILSYQMQ..IHGKQVFWIRLLVVIWC..SAF
Retrocopy SCLGLSIVANF*KTTLFLARVSGAVLTFGPGSLHMFVQTILSYQMQATIHGKQVFWIRLLVVIWCPLSAF

Parental  SMLTCSSLLYSGNFGTDIVQKLHWNPEEKGYVLHMITTAAEWSMSFSFVGFFLTYIRDFQKISLRVEANL
          SMLTCSSLLYSG.F.TDI.QKLHWNPEE.GYVLHMITTA.EWSMS..F.GFFLTY..DFQKIS..VEA.L
Retrocopy SMLTCSSLLYSGSFDTDIAQKLHWNPEEEGYVLHMITTAVEWSMSLAFIGFFLTYSCDFQKIS*QVEASL

Parental  QGLTLYDTVPCPVNNERTRLLSRD
          QGLTLYD...CPVNNE.T.LLSRD
Retrocopy QGLTLYDIAVCPVNNEPT*LLSRD

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_688 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017009	1 retrocopy	retro_dnov_2336,
Loxodonta africana	ENSLAFG00000007736	1 retrocopy	retro_lafr_688 ,
Myotis lucifugus	ENSMLUG00000005097	1 retrocopy	retro_mluc_372,
Mustela putorius furo	ENSMPUG00000004232	1 retrocopy	retro_mputfur_446,
Pteropus vampyrus	ENSPVAG00000005429	2 retrocopies	retro_pvam_1424, retro_pvam_96,