RetrogeneDB ID: retro_lafr_808

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:24310383..24311179(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT6A
• Ensembl ID: ENSLAFG00000012791
• Aliases: None
• Description: None

Sequence

>retro_lafr_808
ATGGCAGGCGTGAAGACCCTGAGCCCCAAAGCCAAGGCGGCACAGCCCAGGCAGCATGGTGGTCAACATCAGCATGGTCC
AGCGGCTACAGGATGTGCTGAGGACCAACCTGGGGCCCGAGAGCACCATGAAGATGCTTGTTTCTGGCGCTGAAGACATC
AAGCTTACTGAAGATGGCAATGTGCTACCTCATGAAATACAAACTCAACACTCAACAGCCCCCTTAATAGCAAAATTAGC
AACAGGCCAGGATGACATAATTGGTGATGGTCCTACTTCCAATGTCCTGATCACTGGAGAGCTGCTGAAACAGGTGGACC
TTTACGCTGAAGGTCTGCATCCCAGAATAATAACTGAAGGATTTGAAGTTGCAAAGGAAAAGGCAATTTAGTGTTTGGAA
CAAATCAAAGTAAACAAAGAGATGGACAGAGAAACACTTATAGACGGGGCCAGAATATGTCTGCATACTAAAGTTCGTGC
CGAACTTGCTGACGTAGTAACAGAGGCTGTAGCTGTCTCCATTTTGGCCATTAAAAAACCTGATGAACTTATTGACCGTT
TCATGGCTGAAATCGTGGAGATGAAATATAAATCTGCAACTGATACAAGCTTAATCAGAGGGCTTGTTTTGGAGCATGGC
ACACAGTATCCTGATACGAAGAAAAGAATAGAAGATGCGTACATCCTCACATGCACTGTGTCATTCTAATATGAAAAAAC
AGAAGTGAACTCTGGCTTCTCTTACAAGAGTGCAGAAGAGAAACTTGCAAAAGCTGAAAGAAAATTCATTGAAGAC

Alignment

ORF - retro_lafr_808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.75 %
• Parental protein coverage: 50.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAVKTLNPKAEVAR-AQAA-LAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQ
          MA.VKTL.PKA..A..AQAA...VNIS....LQDVLRTNLGP..TMKMLVSGA.DIKLT.DGNVL.HE.Q
Retrocopy MAGVKTLSPKAKAAQ<AQAA<MVVNISMVQRLQDVLRTNLGPESTMKMLVSGAEDIKLTEDGNVLPHEIQ

Parental  IQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKEKALQFLEQIK
          .QH.TA.LIAK.AT.QDDI.GDG.TSNVLI.GELLKQ.DLY..EGLHPRIITEGFE.AKEKA...LEQIK
Retrocopy TQHSTAPLIAKLATGQDDIIGDGPTSNVLITGELLKQVDLY-AEGLHPRIITEGFEVAKEKAI*CLEQIK

Parental  VSKEMDRQTLIDVARTSLHTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMVEIMEMKHKSETDTSLIR
          V.KEMDR.TLID.AR..LHTKV.AELADV.TEAV..SILAIKK.DE.ID.FM.EI.EMK.KS.TDTSLIR
Retrocopy VNKEMDRETLIDGARICLHTKVRAELADVVTEAVAVSILAIKKPDELIDRFMAEIVEMKYKSATDTSLIR

Parental  GLVLDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGFFYKSAEEREKLVKAERKFIED
          GLVL.HG...PD.KKR.EDAYILTC.VS..YEKTEVNSGF.YKSAE..EKL.KAERKFIED
Retrocopy GLVLEHGTQYPDTKKRIEDAYILTCTVSF*YEKTEVNSGFSYKSAE--EKLAKAERKFIED

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_808 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 19 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808 ,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,
Tursiops truncatus	ENSTTRG00000015158	1 retrocopy	retro_ttru_1552,