RetrogeneDB ID: retro_lcha_13

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH129019.1:91191..92619(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000003650
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RHBG
• Ensembl ID: ENSLACG00000001771
• Aliases: None
• Description: None

Sequence

>retro_lcha_13
TCCCCCGGCCTGCGGTTCAGGCTGCCTTTTGTGATCATCCTGTTCCAAGCGATCTTCCTGACCCTCTTCAGCCTCTTCGT
GACGTACAACGAACACACAGATGCAGCCGCCCAGACCAATGAGACAGACCACTCTCAAAACGAGCTGTACGAGATCTTCC
CCCTGTTTCAAGATATCCAAGTGATGATCTTCATAGGCTTTGGCTTCCTGATGGCCTTCATGAAGCAGTACGGCTTTGCA
GGCGTGGCCTTCAACTTCTTGACTGCCAACTTCGCCATACAGTGGGCACTGCTCGTGCAAGGGTTCTTCAACCATTACTA
CCATGGTAAGATTCACATTGGCATCTACAACCTCATCAACGCGGAGTTTGCCTGTGCCACCGTCCTGATATCTTTAGGGG
CAGTCCTTGGGAAGGTTAGCCCCATCCAGCTTCTTGTCTTGGCCCTGTTTGAAATCCCCATATATGTGACCACTGAGTGG
ACCATCAGTGAGTACTTGAAAATTAGCGACGTTGGCGGGTCAATGGTTCTCCACGTGTTTGCCTGTTATTTTGGCATGAG
CGTCACCAGGGTTCTTTATAGGCCTGGCCTGAAGGATGGCCATTCAAAAGAAAAGTCATCCTACCAATCAGATCTCTTGG
CAATGATGGGAACCATCTTTCTTTGGATCTTCTGGCCGTCTTTCAACTCTGCATTGGCCAACAGGGGCGATGACCAACAT
CGAGCTGTGATACATACGTACATTGCCCTCAGCTCTTGTACCTTGACTACTTTTGCCTTGACTAGCATGGTGGAAAAGAA
AGGAAAAATCAACATGGCCCTCATTGAGAATGCAACACTCGCTGGAGGAGTGGCTGTCGGAACTTCTGTTGACATGATGG
TCACTCCTGGTGGCGCTTTTATTTTGGGCTGCATCGCCTCCGTGGTGTGCACCCTCGGCTTCAAGTACCTGACTCCATTC
TTGGCCAAGCATCTCAAGATCCAAGACCAGTGCGGCATTCACAACTTGCACGGCATCCCGGGGATCGTAGGGGCCATTGG
GGGCATCATCACCATTCTCCTTTCCAGTGAGGATACCTACGGCCTCAGCCTCTACGAAACGTTCCCGCACCGCGCCCCGG
CCCATGACGACCCAAAGCTCAGCGAAATGGTGCGTCTTCTACCCGTGCTGAAAGCCGGGGCAGGCCGCAGCGCCTCTGAG
CAAGCCCTGTACCAGGCAGCGACTTTAGGGGTTTCCATTGGCGCTTCAGTGCTCGGGGGCTTCCTGACGGGACTTGTACT
CAAGTTGCCTATTTTAGCACAACTGCCGGATGAACATTGCTTCGACGACGAGCCTTACTTTGAGGTTCCAGAGTTGGAGG
AGAAAGAACTGAATCAGATTAAAATAAGCAGTGAGAACTGTGAGGAAAAACTCCGGCTGAACGAAAAT

Alignment

ORF - retro_lcha_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.4 %
• Parental protein coverage: 80.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IHLKLPLTCFFLELITIILFAVFVRYDDETDAKRWHELLKHNKTNLDNDFYYRYPSFQDVHVMIFVGFGF
          ....LP........I...LF..FV.Y...TDA........H......N..Y...P.FQD..VMIF.GFGF
Retrocopy LRFRLPFVIILFQAIFLTLFSLFVTYNEHTDAAAQTNETDHSQ----NELYEIFPLFQDIQVMIFIGFGF

Parental  LMTFLKQYGFGSVGFNFLLASFGIQWATLIQGFLHAFGDDGKIQIGVESMINAEFCTGSVLISFGALLGK
          LM.F.KQYGF..V.FNFL.A.F.IQWA.L.QGF.......GKI.IG....INAEF....VLIS.GA.LGK
Retrocopy LMAFMKQYGFAGVAFNFLTANFAIQWALLVQGFFNHYYH-GKIHIGIYNLINAEFACATVLISLGAVLGK

Parental  TSPVQLLVMTLFETTLFSVNEYILLSIVGAKDAGGAMTIHTFGAYFGLMVSRILYRPNLDKSRQREKSVY
          .SP.QLLV..LFE.......E..........D.GG.M..H.F..YFG..V.R.LYRP.L......EKS.Y
Retrocopy VSPIQLLVLALFEIPIYVTTEWTISEYLKISDVGGSMVLHVFACYFGMSVTRVLYRPGLKDGHSKEKSSY

Parental  HSDVFAMIGTIFLWMFWPSFNSAITAHGDDQHRTVMNTYYSLAACTLATYILSPLVFDDGKISMVHVQNA
          .SD..AM.GTIFLW.FWPSFNSA....GDDQHR.V..TY..L..CTL.T..L...V...GKI.M....NA
Retrocopy QSDLLAMMGTIFLWIFWPSFNSALANRGDDQHRAVIHTYIALSSCTLTTFALTSMVEKKGKINMALIENA

Parental  ALAGGVAAGTAGEMMMNPYGALIVGFLAGVISTLGFQYLTPILDAKLKIQDTCGVHNLHGMPGVLGAVAG
          .LAGGVA.GT...MM..P.GA.I.G..A.V..TLGF.YLTP.L...LKIQD.CG.HNLHG.PG..GA..G
Retrocopy TLAGGVAVGTSVDMMVTPGGAFILGCIASVVCTLGFKYLTPFLAKHLKIQDQCGIHNLHGIPGIVGAIGG

Parental  AVIAALATEEVYGDGMSDVFP
          .....L..E..YG......FP
Retrocopy IITILLSSEDTYGLSLYETFP

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	0.05 RPM	3.82 RPM
DRP000627_kidney	0.05 RPM	1.36 RPM
DRP000627_pectoral_fin	0.00 RPM	10.55 RPM
DRP000627_pelvic_fin	0.00 RPM	3.30 RPM
DRP000627_pharynx	0.03 RPM	0.09 RPM
DRP000627_tail_muscle	0.02 RPM	0.17 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_13 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016811	1 retrocopy	retro_cfam_243,
Latimeria chalumnae	ENSLACG00000001771	1 retrocopy	retro_lcha_13 ,