RetrogeneDB ID: retro_lafr_645

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_28:27355791..27356617(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000016399
• Aliases: None
• Description: None

Sequence

>retro_lafr_645
TCATCATCTGACTCCCAGGAGATGGATTTATGCCATTATAGCATCAAAGTCATTCCTGTGGGGGCAAGTCCTGTAATGAA
GAAGCTCCTCCTGGAGAAGTTCCTCAACATAAGAAGTCTACAGGACCTCAGTGAGCTGCTGGCCATGGGTGCAGGGCTGT
CAGAGATGAGAAAGAACCCAACAGCAAGCACAGCATTAAGGAGCTGCCCTAGGCCATCACGGATGCGGTAACATGTGGGC
CCAACAGAGCACTGTGCAGTGCAGCTCACTGAGATAGGTCATTGGAAGATGCTGCAGCTCACCAAGATCCAGGAAGTTGT
CTGGAGGGGAACACGCTGTTCTGCAATTTCATGCACAAGATGGAGGAGGAGCTGTAGGCCATCCTGGCAGCCAATGAGAG
GCTGTGGCTGAAGTTTCAGAGGTAGGACCAGCAGGCCTGCAATGTGCAGTGCAAGCAGAAGCAGTGGAGAGGCCCACAAG
AAGAGTCTGGTAGGCATGAAGAGGGCATGGGCACAGGCCCATGGGGACAGTGATGCCGAGGGCATGGGAACTCCACTGGA
GGCCAAGAGGGCTGGCTGGCCTGAGGAGAAAGAGGATGAAGCTAAGCATTTCCACCAGGTGGTGGGCAAAGAGCCTGACG
AGGACGTGTTACCAGGGGCTGACCAAGCACAGACAACCTGCTGGGCCACCACCAAAGAAGCAGGATCAGAGACCAGGCTA
AGATGGTAACCAGAGGCCTTCAAAGCTCAAGGGCAGGTCCCATGGATTCCAGACCAACCCCAGAGGGGCTACCTGGGGCC
ATGTGCAGAGCCAGGTGCAGCCACCT

Alignment

ORF - retro_lafr_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.09 %
• Parental protein coverage: 59.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SYNPDSQLDFRHYSIKVVPVGASRGMKKLLQEKFPNMSRLQDISELLATGAGLSESEAEPDGEHNITELP
          S.......D..HYSIKV.PVGAS..MKKLL.EKF.N...LQD.SELLA.GAGLSE....P.........P
Retrocopy SSSDSQEMDLCHYSIKVIPVGASPVMKKLLLEKFLNIRSLQDLSELLAMGAGLSEMRKNPTASTALRSCP

Parental  QAVAGRGNMR-AQQSAVRLTEIGPRMTLQLIKIQEGVG-EGSVLFHSFVHKTEEELQAILAAKEERLRLK
          .....R.........AV.LTEIG....LQL.KIQE.V..EG..LF..F.HK.EEEL.AILAA..ERL.LK
Retrocopy RPSRMR*HVGPTEHCAVQLTEIGHWKMLQLTKIQEVVW<EGNTLFCNFMHKMEEEL*AILAA-NERLWLK

Parental  AQRQDQQAHNVQRKREQ-REAHKKKSLAGMKRMRAEA-DDSDAEDPG----ARREAEPEGEEDEAEYFRQ
          .QR.DQQA.NVQ.K..Q..EAH.KKSL.GMKR..A.A..DSDAE..G....A.R...PE..EDEA..F.Q
Retrocopy FQR*DQQACNVQCKQKQ>GEAH-KKSLVGMKRAWAQAHGDSDAEGMGTPLEAKRAGWPEEKEDEAKHFHQ

Parental  AVGEEPDEDMFP-VLTKQRRPTRPPHKKQRVKDRRPDRDKDQRPPKPKVRSRGAQTKLGPRGAAQGRVQR
          .VG.EPDED..P..LTK.R.P..PP.KKQ...D.RP..D..QRP.K.K.RS.G.QT...PRGA..G.VQ.
Retrocopy VVGKEPDEDVLP>GLTKHRQPAGPPPKKQ---DQRPG*DGNQRPSKLKGRSHGFQT--NPRGATWGHVQS

Parental  QAQLP
          Q.Q.P
Retrocopy QVQPP

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_645 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011989	1 retrocopy	retro_amel_1073,
Loxodonta africana	ENSLAFG00000016399	4 retrocopies	retro_lafr_404, retro_lafr_588, retro_lafr_645 , retro_lafr_666,