RetrogeneDB ID: retro_lafr_406

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:26444954..26445667(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1C1
• Ensembl ID: ENSLAFG00000011909
• Aliases: None
• Description: None

Sequence

>retro_lafr_406
ACTACAAAGAATAACCTTTCTATTACTTCAAAATTCAACATTCCTGATTTAAAGGTTGGCACACTATATGTCTTGGTTGG
TTTGTCAGATGAACTAGCTAAACTGGATGCCTTTGTAGAAGGGGTGGTTACGAAAGTGGCTCGATACATTGCTGATGTGT
TAGAAGACAGTAAAGATAAAGTTGAAGAGAATCTGTTGGCCAATGAAGTTGACTTGGTTACATACTTAACAAGATTCCAG
TGGGACTTGGCCAAATACCCAATCAAGCAGTCCTTGAAAAATACATCTGAAGTAACTGCCAAGGGAATGACTCAGATTGA
CGATGATCCAAAATCTCGAGCATCTGCACACGATAACCTGAAAGGTAACCTTCAGACTCTGGAGCAAACGAATGCAGGAA
GTTGGCTAACTCTAAGTCTAGCAGAAATTGTGAAGAAGGATGACTTAGTTCTTGATGCAGAGTATCTCATCACATTATTG
GTGGTAGTTCCAAAGTTAAACCACAGTGATTGATTAAGCATTCTGAAACACTAGCTGAAATGGTAGTTCCAAGGTCTAGC
AACGTTCTCGCAGAGGACCAAGACAGCTACCTTTGGAATGTCACCTTGTTTAGGAATACAGTTGATGACTTCAGACACAA
AGCCAGGGAAAACAAATTCATTGTTTGTGACTTCCAGTATAATGAAGAGGAAATGAAAGCAGATAAAGAAGAA

Alignment

ORF - retro_lafr_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.17 %
• Parental protein coverage: 62.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKNNNLSVTSKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVVKKVAQYMADVLEDSKDKVQENLLANGV
          T..NNLS.TSKFNIPDLKVGTL.VLVGLSDELAKLDAFVEGVV.KVA.Y.ADVLEDSKDKV.ENLLAN.V
Retrocopy TTKNNLSITSKFNIPDLKVGTLYVLVGLSDELAKLDAFVEGVVTKVARYIADVLEDSKDKVEENLLANEV

Parental  DLVTYITRFQWDMAKYPIKQSLKNISEIIAKKGVTQIDNDLKSRASAYNNLKGNLQNLERKNAGSLLTRS
          DLVTY.TRFQWD.AKYPIKQSLKN.SE..A.KG.TQID.D.KSRASA..NLKGNLQ.LE..NAGS.LT.S
Retrocopy DLVTYLTRFQWDLAKYPIKQSLKNTSEVTA-KGMTQIDDDPKSRASAHDNLKGNLQTLEQTNAGSWLTLS

Parental  LAEIVKKDDFVLDSEYLGTLLVVVPKLNHND-WIKQYETLAEMVVPRSSNVLSEDQDSYLCNVTLFRKAV
          LAEIVKKDD.VLD.EYL.TLLVVVPKLNH.D..IK..ETLAEMVVPRSSNVL.EDQDSYL.NVTLFR..V
Retrocopy LAEIVKKDDLVLDAEYLITLLVVVPKLNHSD<LIKHSETLAEMVVPRSSNVLAEDQDSYLWNVTLFRNTV

Parental  DDFRHKARENKFIVRDFQYNEEEMKADKEE
          DDFRHKARENKFIV.DFQYNEEEMKADKEE
Retrocopy DDFRHKARENKFIVCDFQYNEEEMKADKEE

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_406 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000011909	1 retrocopy	retro_lafr_406 ,
Sarcophilus harrisii	ENSSHAG00000018681	1 retrocopy	retro_shar_89,
Tarsius syrichta	ENSTSYG00000006233	1 retrocopy	retro_tsyr_1134,