RetrogeneDB ID: retro_lafr_351

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_13:1445014..1445878(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCT2
• Ensembl ID: ENSLAFG00000006688
• Aliases: None
• Description: None

Sequence

>retro_lafr_351
GAAGCTGTCCTCAGACTAGAAGGCTCTGGTAATCTGGAGGCAATTCATGTCATCAAGGAGCTAAGAGGAAGTCTGGGAGA
TTTCTATTAAGATGAAGGCTTTCTGTTGCATTAAAAAAAAAAACTGGAGTAAATGAACAAAAGCAAATTGAAAATGCTAA
AATTCTTACAGCAAATACTGGAATGGATACGGACAAAATATAGATATATGGTTCCAGATAAGAGTTGATTCTACAACAAA
GGTTGCAGAAATAGAACAACTTAGGAAAGGAAAAAATGAAGGAGAAAGTTAAATGTATTTTTAAGCATGGAATCAATTGT
TTTATTAACAGGTAATTACTTTATAATTACCCTAAACAGCTCTTCAGTGCTGCTAGTGTCACAGCTATTGAGCATGCAGA
TTTGGTAGGTGTAGAACACCTAGTACTTGTCACAGGTGGTGAAATTGCTTCTGCCTTTGATCACCCAGAACCTGTGAAGT
TTGGAAGTTGCAAACTTGTTGAGGAAGTCATGATTGGAGAAGACAAACTCATTCACTTTTCTGGGGTAGCCCTGGGTAAG
GCTTGCACCATTGTTATGCGTGATGCCACTGAACAAATCTTAAATGAAGCAGAAAGATCTCTCCATGAAGCTCTTTGTGT
TCTTGCTCAAATTGTGAAGAATTTTAAAAGAGTTTATGGAGGAGGCTGCTCTGAGGTCCTGACGGCTCATGCTGTTACAC
AAGGAGCCAACAGAATACCTGGCAAAGAAGCTGCTGCAATGGGGTATTTTGCTAAAGCACTGGGAATGTTGCCAACCATC
ACAGCTGACAATGCAGGCTATGACAGCACAACCCTTGGTAGCACAGCTCCGAGCTGCCCACAGC

Alignment

ORF - retro_lafr_351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.74 %
• Parental protein coverage: 53.56 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EAVLRLKGSGNLEAIHVIKKLGGSLADSYLDEGFLL--DKKI-GVNQPKRIENAKILIANTGMDTDKIKI
          EAVLRL.GSGNLEAIHVIK.L.GSL.D.Y.DEGFLL...KK..GVN..K.IENAKIL.ANTGMDTDKI.I
Retrocopy EAVLRLEGSGNLEAIHVIKELRGSLGDFY*DEGFLLH*KKKL<GVNEQKQIENAKILTANTGMDTDKI*I

Parental  FGSR-VRVDSTAKVAEIEHAE-KEKMKEKVERILKHGINCFINRQLIYNYPEQLFGAAGVMAIEHADFAG
          .GSR..RVDST.KVAEIE....KEKMKEKV..I.KHGINCFINR.L.YNYP.QLF.AA.V.AIEHAD..G
Retrocopy YGSR<IRVDSTTKVAEIEQLR>KEKMKEKVKCIFKHGINCFINR*LLYNYPKQLFSAASVTAIEHADLVG

Parental  VERLALVTGGEIASTFDHPELVKLGSCKLIEEVMIGEDKLIHFSGVALGEACTIVLRGATQQILDEAERS
          VE.L.LVTGGEIAS.FDHPE.VK.GSCKL.EEVMIGEDKLIHFSGVALG.ACTIV.R.AT.QIL.EAERS
Retrocopy VEHLVLVTGGEIASAFDHPEPVKFGSCKLVEEVMIGEDKLIHFSGVALGKACTIVMRDATEQILNEAERS

Parental  LHDALCVLAQTVKDPRTVYGGGCSEMLMAHAVTQLANRTPGKEAVAMESYAKALRMLPTIIADNAGYDSA
          LH.ALCVLAQ.VK....VYGGGCSE.L.AHAVTQ.ANR.PGKEA.AM...AKAL.MLPTI.ADNAGYDS.
Retrocopy LHEALCVLAQIVKNFKRVYGGGCSEVLTAHAVTQGANRIPGKEAAAMGYFAKALGMLPTITADNAGYDST

Parental  A-LVAQLRAAHS
          ..LVAQLRAAHS
Retrocopy T>LVAQLRAAHS

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_351 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000432	2 retrocopies	retro_cfam_1969, retro_cfam_2166,
Choloepus hoffmanni	ENSCHOG00000006098	1 retrocopy	retro_chof_272,
Callithrix jacchus	ENSCJAG00000001715	2 retrocopies	retro_cjac_1854, retro_cjac_2579,
Loxodonta africana	ENSLAFG00000006688	1 retrocopy	retro_lafr_351 ,
Myotis lucifugus	ENSMLUG00000008364	1 retrocopy	retro_mluc_2248,