RetrogeneDB ID: retro_lafr_424

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:7421762..7423015(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEB3
• Ensembl ID: ENSLAFG00000017306
• Aliases: None
• Description: None

Sequence

>retro_lafr_424
ATGGTAGCAGAGTAAGCACTCCAAGTTGTGGAGAAGCTGCAGGCGTGCCTGGCTGTGAACTCCGACTCCAAGAAGTTATT
GATACATTTGAAGAAACTCTCCACATTGACTATTACAGTAGACGTTCTTGCGGAGACTGGGTTTGGGAAAACAGTAAACA
GCTCGTGAAAACACAAGTGCATGGGAAGCTTTGCCAAACATTTAATGGCCCTGTGGAAAGAGCAGGTTCCTGTTGAAAGG
AACACTGAGCTTGACAAACAGCACTTTGAGAAGGTATTTCCCAAAAGTGCTCCAGGAATGCTCTTCTGAAGGAGGAGGAG
TTGAAGGTGGACTACCAAGAAAACTGGAAAGCCTTTGGTAGCCGATCCTACAGCCCTGATCACAGACAGAAAAAAAAAAA
AAAAAGATAACTCTCAAAACATGAGAGACCTCACAAAGTCTCTCACATTCATGAGAGAATGGACAAGAGAAAGAGTGCCA
CAGAGTCTCACCAGCTTGTTCTTCAGACCACAAATCTTCCGATTAAGGCCATGTTCAGTCTCCTCCATCTTCTACCAGTC
TTCATCAGATAGGTGTGGACCACTTCAGATCCCAGGAGGAGGACCATGAACACACTGTTCCATGCCAGAAGCCTGGAAAA
GGCCACAGTAATGCCTTTCAGGACAGTCTGGGAGTCAGCCGAGGACACCTGGGTGAACCCAGAGTAAAGGGGTGGTGACT
CAAAGCGAGGAGCATAAAGCCTCCCACAAGGAAAAATGTCTGTTGGATGCCAAGGGAGATGAAAAGTCTTCCGTTCTGAG
CAGGGAGAAATCACCCAAGGCCGTTTCCAAAGAGGAAAGCTGAAGGCCGCTCTCAGGCAATAACACAAAGGAGAAATCAC
CCTCCAGTGGTGTCAAGAAAGAGGGAGCAGCATCAAGAAAAAGTTTTTGCCTGCCTTAGAGGTTGCTTCAGACAGACACC
TTAAAAAACCAAAGCACAAAGACGCATAGAAAACCAAAAGAGACAAAAATAAGCTAAGTTTAGACACTTTAGACATAAGA
AAGGGGGCAGGAGACCTAGTGCCCAAGCTAAGAGAGAAGGTTTCCAACAATCTTAAGACTCAGGAAGAGAAACTAAAAAC
TTCCAATCTGAATAGAAAATCAGCAAGCTTCCTCCCTAAAGCTAGAGAGGCAGGTATGGATGATGAATCTGAGCAGCCCG
CCATGTCTTTTGAGTCATACCTCAGCTATGACCAGCCCTGGAAGAAAAAGAAA

Alignment

ORF - retro_lafr_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.46 %
• Parental protein coverage: 54.38 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAESALQVVEKLQARLAANPDPKKLLKYLKKLSMLPITVDILAETGVGKTVNSLRKHEHVGSFARDLVA
          M.AE.ALQVVEKLQA.LA.N.D.KKLL..LKKLS.L.ITVD.LAETG.GKTVNS..KH...GSFA..L.A
Retrocopy MVAE*ALQVVEKLQACLAVNSDSKKLLIHLKKLSTLTITVDVLAETGFGKTVNSS*KHKCMGSFAKHLMA

Parental  QWKKLVPVERNTETDEQDFEK-SNSRKRPRDALQKEEEMEVDYQGNWKASGSRSYSPDYRQKKHRK--LP
          .WK..VPVERNTE.D.Q.FEK...S.K..R.AL.KEEE..VDYQ.NWKA.GSRSYSPD.RQKK..K..L.
Retrocopy LWKEQVPVERNTELDKQHFEK<GISQKCSRNALLKEEELKVDYQENWKAFGSRSYSPDHRQKKKKKR*LS

Parental  ELERPHKVSHSHERQDER-KRCHRVSPAYSSDHESSDYGHVQSPPSSTSPHQMCVDHYRSPEEDHVPIVP
          ..ERPHKVSH.HER.D.R.K.CHRVSPA.SSDH.SSD.GHVQSPPSSTS.HQ..VDH.RS.EEDH...VP
Retrocopy KHERPHKVSHIHERMDKR<KECHRVSPACSSDHKSSD*GHVQSPPSSTSLHQIGVDHFRSQEEDHEHTVP

Parental  HQKPGKGHSNAFQDRLGVSQERHLGEP-QSKGVVSQSKEHKSSHKEKRLLDAKGDDKSSALSREKSHKAI
          .QKPGKGHSNAFQD.LGVS...HLGEP.QSKGVV.QS.EHK.SHKEK.LLDAKGD.KSS.LSREKS.KA.
Retrocopy CQKPGKGHSNAFQDSLGVSR-GHLGEP<QSKGVVTQSEEHKASHKEKCLLDAKGDEKSSVLSREKSPKAV

Parental  SKEENRRPFSGDSTKEKPPSSGAKKEKEREGSNIKKKLLPSLEVASDNHLKKPKHKDSEKTKS-DKNKQS
          SKEE..RP.SG..TKEK.PSSG.KKE....G....K.............LK....K...K.K..DKNK.S
Retrocopy SKEES*RPLSGNNTKEKSPSSGVKKE----GAASRKSFCLP*RLLQTDTLKNQSTKTHRKPKE<DKNKLS

Parental  LDSLDTGRGAGDPVPKAKEKASNNLKTQEGKLKTSYLDRKSVGSFPKAEEADMDDEFEQPTMSFESYLSY
          LD.LD...GAGD.VPK..EK.SNNLKTQE.KLKTS.L.RKS....PKA.EA.MDDE.EQP.MSFESYLSY
Retrocopy LDTLDIRKGAGDLVPKLREKVSNNLKTQEEKLKTSNLNRKSASFLPKAREAGMDDESEQPAMSFESYLSY

Parental  DQPRKKKK
          DQP.KKKK
Retrocopy DQPWKKKK

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_424 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011241	1 retrocopy	retro_dnov_1854,
Loxodonta africana	ENSLAFG00000017306	1 retrocopy	retro_lafr_424 ,
Myotis lucifugus	ENSMLUG00000005258	1 retrocopy	retro_mluc_498,
Monodelphis domestica	ENSMODG00000012842	1 retrocopy	retro_mdom_1961,
Sarcophilus harrisii	ENSSHAG00000006165	1 retrocopy	retro_shar_665,