RetrogeneDB ID: retro_lafr_967

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_53:1072069..1072860(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRK4
• Ensembl ID: ENSLAFG00000015019
• Aliases: None
• Description: None

Sequence

>retro_lafr_967
ATCGAAAAGGATTATAGCAGTCTTTGTGACAAGCAGCCGATAGGAAGACTTCTCTTCAGGCAATTCTGTGAAACAAAACC
TGATCTAAACAGATACATTGAGTTCTTGGATGCAGTGGCAGAATATGAAGTGGCCCCTGATGAGCACCAAAGAGACTGTG
GACTGAAGGTCCTAGGTACGTTCTTCAGTGAGGATACGCATGAAGCCCCTTTACCAGAAATACCTCAGGATGTTGTGACA
AAGTGTAAAGAGAGACTAGAAGAGGACTCTTCCAAGGAAGTCTTCGAGGAATGCACTAGAATTGTCCATAACTATTTAAG
TGGAAAACCATTTGAAGAATACCAAGAAAGCTCATATTTTTCTCAGTTTTTACAGTGGAAATGGCAGGAAAGGCAACCAG
TAACAAGGAGCACATTTAGACATTACAGAGTTCTAGGAAAAGGTGGATTTGGAGAGGTGTGTGCCTGCCAAGTGCGAGCT
ACAGGAAAAATGTATGCCTGTAAAAAAAACTAGAGAAGAAGAGGATAAAGAAGAGGAAAGGTGAAGCCATGGCTCTGAAC
GAGAAAAGAATCTTAGAAAAAGTGCACAGCAGATTTGCAGTTAGTTTATCCTACACGTAAGAAACCAGAGACGCCGTGTG
CTTGGTGCTAACCATCATGCATGGAGGGGATCTGAAGTTTCACATCTATAACCTGGGCAATCCTGGCTTTGATGAGCACA
GAGCTGTGTTCTATGCTGCAGAGCTGTGCTGTGGCTTGGACGATTTACAGCAGGAAAGAATTGTGTACAGA

Alignment

ORF - retro_lafr_967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.99 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEKDYSSLCDKQPIGRLLFRQFCETKPDLNRCIEFLDAVAEYEVAPDEHQRDCGLKVLASVLKIQTPEAP
          .EKDYSSLCDKQPIGRLLFRQFCETKPDLNR.IEFLDAVAEYEVAPDEHQRDCGLKVL.......T.EAP
Retrocopy IEKDYSSLCDKQPIGRLLFRQFCETKPDLNRYIEFLDAVAEYEVAPDEHQRDCGLKVLGTFFSEDTHEAP

Parental  LLEIPQDVVTKCKERLEEDPSKEVFEECTRIVHKYLSGKPFEEYQESSYFSQFLQWKWRERQPVTRRTFR
          L.EIPQDVVTKCKERLEED.SKEVFEECTRIVH.YLSGKPFEEYQESSYFSQFLQWKW.ERQPVTR.TFR
Retrocopy LPEIPQDVVTKCKERLEEDSSKEVFEECTRIVHNYLSGKPFEEYQESSYFSQFLQWKWQERQPVTRSTFR

Parental  HYRVLGKGGFGELCAQCLVPLPSLCFLSKRTYARICVRR-LNGMKLSIRVAKLYEASNSTFTVSALLSYT
          HYRVLGKGGFGE.CA.C.V.........K....R...RR...G...........E...S.F.VS..LSYT
Retrocopy HYRVLGKGGFGEVCA-CQVRATGKMYACKKN*RRRG*RR<RKGEAMALNEKRILEKVHSRFAVS--LSYT

Parental  YETRDALCLVLTIMNGGDLKFHIYNLGNPGFDEHRAVFYAAELCCGLDDLQRERIVYR
          .ETRDA.CLVLTIM.GGDLKFHIYNLGNPGFDEHRAVFYAAELCCGLDDLQ.ERIVYR
Retrocopy *ETRDAVCLVLTIMHGGDLKFHIYNLGNPGFDEHRAVFYAAELCCGLDDLQQERIVYR

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_967 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000015019	1 retrocopy	retro_lafr_967 ,
Pan troglodytes	ENSPTRG00000015853	1 retrocopy	retro_ptro_805,