RetrogeneDB ID: retro_lcha_58

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127037.1:104966..105656(-)
• Located in intron of: ENSLACG00000003978

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000012745
• Aliases: None
• Description: None

Sequence

>retro_lcha_58
CTCATGAATTTCAACTTGAAAATAAAGAACTCCACAAAAGGTTTTTCAACAAAGCAGGCATTGATTAAACTTCAGAAGAG
CAAATTGTCAGATCACAAAACACAAATATTTTATAACGGAGCTAGGGCATTTTTAAGTGCTTCAGCTACGTATCTACAAC
ATAAATTGCCATTTAATGATGCAGTTTTGCAAAATAGCCAGTTTGTGGATATAAGCAAAGGACAGGCAACATTTGGCCAA
GTGGAATACTTTTGTACCAGGTTTTCAGAAACTCTACAACTTTCAGCAAGTGACATGGATTGCTTGTTTGACCAATTCCA
GGATTTTCAGTCTCATGTTGAAGATAAATATTTATATCAATCAGCTGATGTAGTGACATTTTGGAGCAACCTCATGGATA
TTACAGATTGCAATAGACATAAGCAATTTGACAAACTAAAGTAGTTTTTTTTAGTTCTTGTGCTTCCACATAGTAACTCA
GGTGAAGAACGAGTCTTCAGTATTATTAAGAAAAACAAAACAGAATGTTGGAGTACCATGCAAAACAATACACTGTCTTC
TTTGCTTAGCTGTAAAATAAATGCCCTTGATGATATAAAATGCTTTCAGTATGTTCCCAGCAAAGAAATTAAGAAAAGGG
CAAAATCTGTTACAAAAGTATACAATAATTTGCATGCATCAAAGAAAAAC

Alignment

ORF - retro_lcha_58 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 53.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LENKELYIGFSTKQALIKLQKDTYLPNHSLSDHKTQIFYNGARAFLNASAMYLQQKLPFNDRVLQNSQFV
          L.N..L.I..STK....K.Q....L....LSDHKTQIFYNGARAFL.ASA.YLQ.KLPFND.VLQNSQFV
Retrocopy LMNFNLKIKNSTKGFSTK-QALIKLQKSKLSDHKTQIFYNGARAFLSASATYLQHKLPFNDAVLQNSQFV

Parental  DISRGQATFGQVEYFCARFSETLQLSASAMDCLFDQCQDFQSYVKDKYLYQSVDVVTFWSNLMDVTDCNG
          DIS.GQATFGQVEYFC.RFSETLQLSAS.MDCLFDQ.QDFQS.V.DKYLYQS.DVVTFWSNLMD.TDCN.
Retrocopy DISKGQATFGQVEYFCTRFSETLQLSASDMDCLFDQFQDFQSHVEDKYLYQSADVVTFWSNLMDITDCNR

Parental  HKRFDKLCKVAFLVLVLPHSNSGEEQVFSIIKENKT-MRSAMQNNMLSSLLSCKINSLDDTKWFQYVPSK
          HK.FDKL.K....VLVLPHSNSGEE.VFSIIK.NKT...S.MQNN.LSSLLSCKIN.LDD.K.FQYVPSK
Retrocopy HKQFDKL-K*XXXVLVLPHSNSGEERVFSIIKKNKTECWSTMQNNTLSSLLSCKINALDDIKCFQYVPSK

Parental  EIKKRAKSVTKVYNNLHASKKN
          EIKKRAKSVTKVYNNLHASKKN
Retrocopy EIKKRAKSVTKVYNNLHASKKN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	0.07 RPM	0.00 RPM
DRP000627_kidney	0.00 RPM	0.00 RPM
DRP000627_pectoral_fin	0.00 RPM	0.16 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.10 RPM	0.00 RPM
DRP000627_tail_muscle	0.19 RPM	0.00 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_58 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Latimeria chalumnae	ENSLACG00000012745	1 retrocopy	retro_lcha_58 ,