RetrogeneDB ID: retro_lafr_668

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:2354245..2355098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGGT1B
• Ensembl ID: ENSLAFG00000003752
• Aliases: None
• Description: None

Sequence

>retro_lafr_668
AATGTAACTTGCTGTGGCTTCCCAAGCTGTTGATACCTGAGTATCCCAATCAATCTATCAAAGAATCCTGGGGCAGCTCA
TCCTTATGACAGTGGCCACATAGCAACAACCTGACTGGGCTTTCATGCTTAGTTATTCTCAGAGACAACTTAAACAGATT
AAATAAAGAAGCTTGTTTACGAGGCTTGAGAACCCTTTTGCTAGAAGAGGGGAGTTTTTGTGCTCTCTCTGGAGGAAATC
AAAATGATATGCAATTTGTGTGCTATGCTTTCTGTGGTTGTTATATGCTCAACAGCTGTCAGCCATGGATATGAGAACAG
CTATTGACTACATTAGAAGAAGTATATCCTATGACGATGGACTTGCACAGGGGGCTGGGCACTTATCTCATGGGGGAGCC
ACTTTTTGTGGCATAGCTTCACTGTGTCTGATGGGTAAAGCCGAAAAAAAGTTTTTCAGAAAAGGAACTGAACAGGATAA
AGAGGTGGTATATAAAGAGGCAAAAAATGATTACCATGGAAGACCTGATTAACCTACATAACCTGTTATTCTTTATGGTT
GGAAACAACTCTGAAAATTTTCTAATGCGCTAACTTGGAAAAAATAAAAATTACATCTTACCATCCCAAGATTGCCCTGT
AGAAGGACTTGGCAAGTGGTTATATAGTCATCCAGATGCTTTGCATGCAAACTTTGGGATTTGTGGCCTGTCACTAATGG
AGGAAAGTAGAATTTGAAAAATACACCCTGCCCTGAATGTAAGGACACAGACTTCTAAATGCCTTGGAGATCTCAAGCAT
ATTGGAAAACCAAGGCTTCTAAACAATGTTCAGAGAATGTGCATATCTCCACA

Alignment

ORF - retro_lafr_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.57 %
• Parental protein coverage: 76.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  NLNRCGFRGSSYLGIPFNPSKNPGTAHPYDSGHIAMT-YTGLSCLVILGDDLSRVNKEACLAGLRALQLE
          N...CGF....YL.IP.N.SKNPG.AHPYDSGHIA.T..TGLSCLVIL.D.L.R.NKEACL.GLR.L.LE
Retrocopy NVTCCGFPSC*YLSIPINLSKNPGAAHPYDSGHIATT<LTGLSCLVILRDNLNRLNKEACLRGLRTLLLE

Parental  DGSFCAVPEGSENDMRFVYCASCICYMLNNW-SGMDVKKAIDYIRRSMSYDNGLAQGAGLESHGGSTFCG
          .GSFCA...G..NDM.FV..A.C.CYMLN...S.MD...AIDYIRRS.SYD.GLAQGAG..SHGG.TFCG
Retrocopy EGSFCALSGGNQNDMQFVCYAFCGCYMLNSC<SAMDMRTAIDYIRRSISYDDGLAQGAGHLSHGGATFCG

Parental  IASLCLMGKLE-EVFSEKELNRIKRWCIMRQ-QNGYHGRPNKPV-DTCYSFWVGATLKLLKIFQYTNFE-
          IASLCLMGK.E...FSEKELNRIKRW.I.RQ..N.YHGRP..P...TCYS.W...TLK...IF...N.E.
Retrocopy IASLCLMGKAE>KSFSEKELNRIKRWYIKRQ<KNDYHGRPD*PT<ITCYSLWLETTLK---IF*CANLE<

Parental  KNRNYILSTQDRLVGGFAKWPDSHPDALHAYFGICGLSLMEESGICKVHPALNVSTRTSERLQDL-HQSW
          KN.NYIL..QD..V.G..KW..SHPDALHA.FGICGLSLMEES.I.K.HPALNV.T.TS..L.DL....W
Retrocopy KNKNYILPSQDCPVEGLGKWLYSHPDALHANFGICGLSLMEESRI*KIHPALNVRTQTSKCLGDL<QAYW

Parental  KAQDSKQCSENVHIST
          K...SKQCSENVHIST
Retrocopy KTKASKQCSENVHIST

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_668 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016700	1 retrocopy	retro_cjac_1058,
Cavia porcellus	ENSCPOG00000002443	1 retrocopy	retro_cpor_1344,
Homo sapiens	ENSG00000164219	2 retrocopies	retro_hsap_675, retro_hsap_698,
Loxodonta africana	ENSLAFG00000003752	1 retrocopy	retro_lafr_668 ,
Pongo abelii	ENSPPYG00000015694	3 retrocopies	retro_pabe_527, retro_pabe_545, retro_pabe_640,
Pan troglodytes	ENSPTRG00000017146	2 retrocopies	retro_ptro_444, retro_ptro_487,