RetrogeneDB ID: retro_lafr_388

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_14:34432222..34433070(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GHITM
• Ensembl ID: ENSLAFG00000009646
• Aliases: None
• Description: None

Sequence

>retro_lafr_388
GGGAAAGCCGGTCAAAACCTCAAAGAGGCTTCACTGGAACCGTCAATGAGAAAAACATTTAAAACTGATCAGATGGGAAG
ATGGTTTGTCGCTGGAGAGGCTGCTGTTGGTCTTAACACATTGTGCTTCTGTGGCGTGAGAATGTCTAATGAGACTGGAG
CTGTTGGAAAGGTTGTAATCTGGCCCCAGTCTGTGAAAGATAGAATTCATTCTACCCATATGTACCTAGCTGGAGGTATT
GGTTTAACAGCCTTGTCTGCCTTGGCAGTAAGCAGAAATCCTGTTTTCATGAACTTCATGATGAGAGGCTCTTGGGTGAC
AACTGGTGCAACCTTTGCAGTCATGACTGGAGCTGGAACGCTGGTACAATCGATATCATGTCATAATAGCCCAGGCCCAA
AGCATCTTGCTTAATCACTACATTCTGGTATGATGGGCGCAGTGGTAGCTCCTCTGATGATATTAGGGCAGCCTCTTATC
AGAGGTGCATATCACACATCTGACATTGTGGCCATATGCGCTCTCTGTGAGAAGCTTCTGAACATGGGAGCACCCTCAGA
GCGGGTCTAGGTCTTGTCTTCATGTCCTCACCGGGATCTATGTTTCTTCCATCTACCACTGTGGCTGGTGCCACACTGCA
TTCAGTGGCAATTTATAGCGTATTAGTTCTTCTCAGCATGTTCCTTCAGTCTGATGCCCAGAAAATAATCAAGCACACAG
AAATGGCACCCATATATGGAATTCAAAAATATGATCCCATCAATTCAATCATGGGAACCAACATGGAGGCATTAAATAAA
TTTATGCTAGTTGTCAGCATGCTAGAAACTGGAAGCAACAGAAAGAAA

Alignment

ORF - retro_lafr_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.76 %
• Parental protein coverage: 84.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKTVQELKEAALEPSMEKIFKIDQMGRWFVAGGAVVGLGALCYYGLGMSNEIGAIEKAVIWPQYVKDRIH
          GK..Q.LKEA.LEPSM.K.FK.DQMGRWFVAG.A.VGL..LC..G..MSNE.GA..K.VIWPQ.VKDRIH
Retrocopy GKAGQNLKEASLEPSMRKTFKTDQMGRWFVAGEAAVGLNTLCFCGVRMSNETGAVGKVVIWPQSVKDRIH

Parental  STYMYLAGSIGLTALSALAVTRSPVLMSFMMRGSWVTIGATFAAMIGAGMLVHSIPYHQSPGPKHLAWLL
          ST.MYLAG.IGLTALSALAV.R.PV.M.FMMRGSWVT.GATFA.M.GAG.LV.SI..H.SPGPKHLA..L
Retrocopy STHMYLAGGIGLTALSALAVSRNPVFMNFMMRGSWVTTGATFAVMTGAGTLVQSISCHNSPGPKHLA*SL

Parental  HSGVMGAVVAPLAILGGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAP-LGVGLGLVFVSSLGSMF
          HSG.MGAVVAPL.ILG.P.LIR.A..T..IV......A.C...EK.LNMGAP.L..GLGLVF.SS.GSMF
Retrocopy HSGMMGAVVAPLMILGQP-LIRGAYHTSDIV---AICALC---EKLLNMGAP<LRAGLGLVFMSSPGSMF

Parental  LPPTTVAGATLYSVAVYGGLVLFSMFLLYDTQKVIKRAEIVPTYGVQKYDPINSMMGIYMDTLNIFMRVV
          LP.TTVAGATL.SVA.Y..LVL.SMFL..D.QK.IK..E..P.YG.QKYDPINS.MG..M..LN.FM.VV
Retrocopy LPSTTVAGATLHSVAIYSVLVLLSMFLQSDAQKIIKHTEMAPIYGIQKYDPINSIMGTNMEALNKFMLVV

Parental  TMLASGGNRKK
          .ML..G.NRKK
Retrocopy SMLETGSNRKK

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_388 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388 ,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,