RetrogeneDB ID: retro_lcha_62

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127072.1:438869..440072(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LHCGR
• Ensembl ID: ENSLACG00000011376
• Aliases: None
• Description: None

Sequence

>retro_lcha_62
AATTGGCATCACATGTGCAACAAATCCCAACTCAAGTTGGATAAGTCGAAGCAACGAGGATCTACTGTAGATGAAGAATA
TGTTCCTTTTGAGTATGGACTTGAATTTATGGAAGACGACTATGACCCTCATTTTGATTATGACTTTTGTCGTGAAATGC
TACATGTGGACTGTTCTCCCAAACCAGATGCATTTAATCCATGTGAAGATATTATGGGATATGATGTCCTAAGGATCCTC
ATATGGTTCATTAACATACTAGCCATCACTGGAAATATTGTAGTGTTAGCAGTTTTACTAACTAGTCGATATAAGCTCAC
TGTCCCTCGATTTCTCATGTGCAATCTTGCATTTGCAGACTTGTGTATGGGAGTTTACTTGTTGCTTATTGCCTCTGTAG
ATATTATGACTAAAAATAAATACTACAACTATGCAATAGACTGGCAGACCGGTGCTGGTTGTGGTGCAGCAGGGTTTTTC
ACAGTTTTTGCAAGTGAGCTCTCTGTGTATACCTTGACAGTGATTACTTTGGAAAGATGGCATACAATTACCAATGCTAT
GCAACTAGATAGAAGAGTCCGTATTAAACATGCTACAGTTATCATGATTGGTGGCTGGATTTTTGCTTTTACTGTGGCCT
TCCTTCCTGTTGTTGGAGTTAGCAGCTACATGAAGGTTAGCATCTGTCTGCCCATGGACATAGAAACATCACTTTCTCAA
GCTTATATCGTCTTCATTTTGATTCTTAATGTCCTTGCATTTATAATAATTTGTGCCTGCTACTTTAAAATCTACCTTAC
AGTAAGAAATCCTCATTTTGTTTCTACAAATAGTGATACAAAGATAGCCAAGCGCATGGCAGTATTGATCTTCACTGATT
TTGTCTGCATGGCACCTATATCATTCTTTGCCATCTCAGCATCCTTTAAAGTCCCCCTCATTACTGTGTCCAAATCTAAG
ATCATTTTGGTATTGTTCTACCCAATAAATTCCTGTGCCAATCCTTTCCTTTATGCTATTTTCACAAAGACATTCCGGAG
AGATTTTTTCATTCTGATGAGCAGGTTTGGTTGTTGTGAAATGCAAGCCCAGATTTATAGAACTGAAACAACATCCTCCG
TTCATAATACAAGAAATGGTACATGGGCACCTACACAAAAAATCAGTGAGGGTACATTATCTGTGCTGGTGCCTCTCAAT
CAC

Alignment

ORF - retro_lcha_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.41 %
• Parental protein coverage: 68.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLSRQCESSATRSPYADETLKKTDKTYPPDNYSVILEEENEGISFDFDYDFCQTKMNLRCTPVPDAFNPC
          N....C..S..............D..Y.P..Y...LE.........FDYDFC.......C.P.PDAFNPC
Retrocopy NWHHMCNKSQLKLDKSKQRGSTVDEEYVPFEYG--LEFMEDDYDPHFDYDFCREMLHVDCSPKPDAFNPC

Parental  EDIMGYDFLRILIWFINILAITGNIIVLLVLLTSRYKLTVPRFLMCNLSFADLCMGLYLLLIASVDSKTR
          EDIMGYD.LRILIWFINILAITGNI.VL.VLLTSRYKLTVPRFLMCNL.FADLCMG.YLLLIASVD..T.
Retrocopy EDIMGYDVLRILIWFINILAITGNIVVLAVLLTSRYKLTVPRFLMCNLAFADLCMGVYLLLIASVDIMTK

Parental  SQYYNHAIEWQTGAGCNTAGFFTVFASELSVYTLTVITLERWHTITYAMQLERNLRLRHAIMIMIGGWIF
          ..YYN.AI.WQTGAGC..AGFFTVFASELSVYTLTVITLERWHTIT.AMQL.R..R..HA..IMIGGWIF
Retrocopy NKYYNYAIDWQTGAGCGAAGFFTVFASELSVYTLTVITLERWHTITNAMQLDRRVRIKHATVIMIGGWIF

Parental  SLSMALLPIAGISNYMKVSICLPMDIETSVSQAYILIILVLNVIAFLVVCICYVKIYLSVQNPDFAAKNK
          ....A.LP..G.S.YMKVSICLPMDIETS.SQAYI..IL.LNV.AF...C.CY.KIYL.V.NP.F...N.
Retrocopy AFTVAFLPVVGVSSYMKVSICLPMDIETSLSQAYIVFILILNVLAFIIICACYFKIYLTVRNPHFVSTNS

Parental  DTKIAKRMAILIFTDFTCMAPISFFAISAAFKVPLITVTNSKILLVLFYPINSCANPFLYAIFTKAFRRD
          DTKIAKRMA.LIFTDF.CMAPISFFAISA.FKVPLITV..SKI.LVLFYPINSCANPFLYAIFTK.FRRD
Retrocopy DTKIAKRMAVLIFTDFVCMAPISFFAISASFKVPLITVSKSKIILVLFYPINSCANPFLYAIFTKTFRRD

Parental  FFILLSRFGCCKTQAELYRVSTLSAYNLNFRKHSSLAGANKNSQRNTFVLVPSHH
          FFIL.SRFGCC..QA..YR..T.S............A...K.S.....VLVP..H
Retrocopy FFILMSRFGCCEMQAQIYRTETTS--SVHNTRNGTWAPTQKISEGTLSVLVPLNH

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	0.11 RPM	0.05 RPM
DRP000627_pectoral_fin	0.00 RPM	0.16 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.02 RPM	0.00 RPM
DRP000627_tail_muscle	0.02 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_62 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	ENSLACG00000011376	1 retrocopy	retro_lcha_62 ,