RetrogeneDB ID: retro_lafr_978

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_551:4099..5462(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESCO2
• Ensembl ID: ENSLAFG00000001229
• Aliases: None
• Description: None

Sequence

>retro_lafr_978
GCTAAATGTCAACCAAGTTATAAGTGCATCAAACCTGTATCAAGGAATTCTAGAAATTCCAAGCAAAATAGAGTAGCTTA
TAAGCCAATTGTGGGGAAAGAGAATAAATGTTATTCAGTTGAAAATAATCTGAATACTCCTTGAGTATTAAGCCAAAAAA
TAAAACCACAAGTTACACTCCAGGGTGGAGTGGCATTTTTTGTTAGTAGAAAAAAATCTTCCCTTAGAAAATTGTCTCTG
GAGAATAAGTCATTACTGGGACCTACTGGAAAGAATAAATCAGAAGTGATTGAAGATTCTGATGTAGCGACTGCCCATGA
AAGAAAAACTTTTGAGACAAGGCAAGTGCCTAAGTGCTTGTTAAAGGAACTGAACATGGAGCTACTGGGTGCAAGAAGTA
AAAATGAGAAATTAATGAAAGATTCATCAGGTGGAGTAGTATCTTCGAGAGGATATAAACTTGATGAAAATAAGCATTTC
CCTTAGAGGATACCCTCAGTGAGAACAAGGCAGCTGCTCCAGAGTCCATTGTGTACCCCATTTTCACTGTGTCTTCAGTC
AATACAAAAAGATCTCTACCTGAAGAACAATCTTCTATGGGCTCCATTGTATCTACTAACTTCTTGAAACAGACCAGCTT
GCAGAATAATGCCAGAGATACAAATAAAGAAATAAAAGACCAGTTCATCATTGATGCAGGTCAGAAGCATTTTGGGGCCA
CTACGTGCAAGTCTTGTGGCATGATCTACACTGCTTCCAACCCTGAAGATGAACTGCAGCATGCTCAGTATCACCAGAGA
TTTCTGGAGGGAATCAAATATGCAGGTTGGAAGAAAGAACGCATAGTTGAGAGTTTTGGGATGGAAAAATTGTGTTGGTC
CTGCCACATGATCCAAATTATGCTATCAGGAAGGTAGAAGATGTCCAAGAACTTGTCGATGATGAACTGGGATTCCATCA
AGTTATTCCTAGATGTCCAAACAAAACCAAAACTTTTCTCTTTATATCTGATGAAAAGAAAGTAGTTGGGTGATTAATTG
CAGAGCCCATCAAACAGGCTTTCCGTGTTCTATCTGAACCAACTGGTCCAGAATCCCCAAGCTCTAAAGAATGTCACAGG
GCTTGGCAATGTTCAAATGTACCACAGCCTGCAGTCTGTGGGATAAGTAGAATCTGGGTCTTCAGACTGAAGAGAAGAAA
GCGCATTGCAAGACAACTAGTAGATACTCTCAGGAATTGCTTCATGTTTGGCTGTTTTCTCAGCACTGATGAAATTGCAT
TTTCTGACCCAACTCCAGACGGCAAATTATTTGCAACCAAGTACTGCAACACCCCTAATTTCCTTGTATCCAATTTTAAT
AGT

Alignment

ORF - retro_lafr_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.28 %
• Parental protein coverage: 73.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKCQPSYKCIKPVSRNSRNSKQNRVAYKPIVGKENKCYSVENNLNAPRVLSQKIKPQVTLQGGAAFFVSR
          AKCQPSYKCIKPVSRNSRNSKQNRVAYKPIVGKENKCYSVENNLN.P.VLSQKIKPQVTLQGG.AFFVSR
Retrocopy AKCQPSYKCIKPVSRNSRNSKQNRVAYKPIVGKENKCYSVENNLNTP*VLSQKIKPQVTLQGGVAFFVSR

Parental  KKSSLRKLSLENKSLLGPTGKNKSEVIEDSDVATTHERRTFETRQVPKCLLKELNMELLGARSKNEKLMK
          KKSSLRKLSLENKSLLGPTGKNKSEVIEDSDVAT.HER.TFETRQVPKCLLKELNMELLGARSKNEKLMK
Retrocopy KKSSLRKLSLENKSLLGPTGKNKSEVIEDSDVATAHERKTFETRQVPKCLLKELNMELLGARSKNEKLMK

Parental  DSSGGVVSSRGYKVDENKHFP-LEDTLSENKAAAPESIVYPIFTVSSVNTKRSLAEEQSSMGSIVSTNFL
          DSSGGVVSSRGYK.DENKHFP.LEDTLSENKAAAPESIVYPIFTVSSVNTKRSL.EEQSSMGSIVSTNFL
Retrocopy DSSGGVVSSRGYKLDENKHFP<LEDTLSENKAAAPESIVYPIFTVSSVNTKRSLPEEQSSMGSIVSTNFL

Parental  KQTSMQKNARDTNKEIKDQFIIDAGQKHFGATTCKSCGMIYSASNPEDELQHAQYHQRFLEGIKYAGWKK
          KQTS.Q.NARDTNKEIKDQFIIDAGQKHFGATTCKSCGMIY.ASNPEDELQHAQYHQRFLEGIKYAGWKK
Retrocopy KQTSLQNNARDTNKEIKDQFIIDAGQKHFGATTCKSCGMIYTASNPEDELQHAQYHQRFLEGIKYAGWKK

Parental  ERVVA-EFWDGKIVLVLPHDPNYAIRKVEDVQELVDDELGFHQVIPRCPNKTKTFLFISDEKKVVGCLIA
          ER.V..EFWDGKIVLVLPHDPNYAIRKVEDVQELVDDELGFHQVIPRCPNKTKTFLFISDEKKVVG.LIA
Retrocopy ERIVE<EFWDGKIVLVLPHDPNYAIRKVEDVQELVDDELGFHQVIPRCPNKTKTFLFISDEKKVVG*LIA

Parental  EPIKQAFRVLSEPTGPESPSSKECHRAWQCSNVPQPAVCGISRIWVFRLKRRKRIARRLVDTLRNCFMFG
          EPIKQAFRVLSEPTGPESPSSKECHRAWQCSNVPQPAVCGISRIWVFRLKRRKRIAR.LVDTLRNCFMFG
Retrocopy EPIKQAFRVLSEPTGPESPSSKECHRAWQCSNVPQPAVCGISRIWVFRLKRRKRIARQLVDTLRNCFMFG

Parental  CFLSTDEIAFSDPTPDGKLFATKYCNTPNFLVYNFNS
          CFLSTDEIAFSDPTPDGKLFATKYCNTPNFLV.NFNS
Retrocopy CFLSTDEIAFSDPTPDGKLFATKYCNTPNFLVSNFNS

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_978 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000001229	1 retrocopy	retro_lafr_978 ,
Rattus norvegicus	ENSRNOG00000015921	1 retrocopy	retro_rnor_85,