RetrogeneDB ID: retro_lcha_61

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127065.1:886119..886833(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000013617
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: plin2 (7 of 7)
• Ensembl ID: ENSLACG00000017943
• Aliases: None
• Description: perilipin 2 [Source:ZFIN;Acc:ZDB-GENE-050913-12]

Sequence

>retro_lcha_61
GCTGAGGTAGAAGCTGAAACTCCACAGAATGTGGTTGTCCGAGTTGCTAATCTTCCTCTGGTTAGTTCCACTTATGATAT
GGTGTCCTCTGTCTATGTTAATACAAAAGAGAATCATCCTTACCTGAGATCAGTCTGTGAAGTGGCAGAAAAAGGCGTGA
AGACAATCGGAGCAGCTGCTTTTACTAATGCTATACCAGTCATCCAGAAAATGGAGTCCTTCGTTGTGATTGCCAATAAC
TATGGAAACATAGCTCTGGACAAGGTTGAAGAGAAACTGCCCATTTTACATCAGCCCTCTGACAAGGTGGTTACTATTGC
TAAGGAACTGGTGATGGGTGCAAAGGAGACTGTTGACCACACAATCTTTGGGGTGGTAGACCACACGAAAGAAGCTGTGC
ATGGAAGTATAGAGATGGCCAAATCTGTTGTGACTGGTGGTGTCGACACTGTTTTTGGAAGCCATGTAGTTCCAGTTGTG
AGCAGTGGTGTAGCTGCTGCACTGACCAAGTCTGAACTCTTTGTGGATCACTATTTTCCCTTGACAGAAGATGAATTGGA
ATCTGTAGAGGCTGAAGGATATGAAAGTGGAACGCCAAACTACTACATGAGACTGAGATCCTTGTTGTTCAAAGTGTGGA
AACATGCCTCTTGGCAGGCCTGGTCTAGAATCCGGGATGCCAAACAAAGAAGCTAAGAGGTCATTACCCAGATC

Alignment

ORF - retro_lcha_61 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 89.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASVGADTPQNVVVRVANLPLVSSTYDMVSSVYVNTKENHPYLRSVCEVAEKGVKTITAAAFTNAIPFIQK
          A.V.A.TPQNVVVRVANLPLVSSTYDMVSSVYVNTKENHPYLRSVCEVAEKGVKTI.AAAFTNAIP.IQK
Retrocopy AEVEAETPQNVVVRVANLPLVSSTYDMVSSVYVNTKENHPYLRSVCEVAEKGVKTIGAAAFTNAIPVIQK

Parental  MEPQIVFVNNYASIVLDKVEEKLPILRQPSDKVATNAKGLVMGAKEVV-HTISGVVDKTKEAVHESMETA
          ME...V..NNY..I.LDKVEEKLPIL.QPSDKV.T.AK.LVMGAKE.V.HTI.GVVD.TKEAVH.S.E.A
Retrocopy MESFVVIANNYGNIALDKVEEKLPILHQPSDKVVTIAKELVMGAKETVDHTIFGVVDHTKEAVHGSIEMA

Parental  KSIVNGGVNTVFGNHVVQIISSGVDAALTKSELFVDHYLPLTEDELAKESAEAEGYESGTPNYYMRLRSL
          KS.V.GGV.TVFG.HVV...SSGV.AALTKSELFVDHY.PLTEDEL..ES.EAEGYESGTPNYYMRLRSL
Retrocopy KSVVTGGVDTVFGSHVVPVVSSGVAAALTKSELFVDHYFPLTEDEL--ESVEAEGYESGTPNYYMRLRSL

Parental  LFKVCKYAYWQALSRIRDAKQISQEIFTQI
          LFKV.K.A.WQA.SRIRDAKQ.S.E..TQI
Retrocopy LFKVWKHASWQAWSRIRDAKQRS*EVITQI

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	1.07 RPM	0.00 RPM
DRP000627_kidney	0.59 RPM	0.00 RPM
DRP000627_pectoral_fin	2.43 RPM	0.02 RPM
DRP000627_pelvic_fin	2.28 RPM	0.00 RPM
DRP000627_pharynx	0.20 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_61 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002827	1 retrocopy	retro_amel_321,
Callithrix jacchus	ENSCJAG00000008088	1 retrocopy	retro_cjac_2494,
Latimeria chalumnae	ENSLACG00000017943	1 retrocopy	retro_lcha_61 ,