RetrogeneDB ID: retro_lcha_123

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH130124.1:22500..23122(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLACG00000016958
• Aliases: None
• Description: None

Sequence

>retro_lcha_123
ATGGCAACTGGTGGTAGTGAAAGCGAGTACTTCACCACCTACAACGTAGTGCTTGTTGGAGATGCAAATGTGGGTAAAAG
TGCCCTGGGTATACAGTTTTCTTATGGTTTCTTCATATCGGAGTTACACCCAACAGTTACGGACTCTTACATGAAACGTG
CAGAAATAGATGGTCAGGTAGCCATTATTGATGTTCTAGATGCAGCAGGGTTAGAGGAGTTCAGTGCATTGCAGGATTGG
TACTTGAGGACAGGAGAAGGGTTCCTCCTAGTTTATTCAGTAACAGATGAGAAAAGTTTCCAGCAAGTGCAGTGGTTACA
TGAGCTTATTCTCAGAACGAAAGACAGAGATTCTTTTCCAATGATCCTGGTGGCAAACAAGGTGGATCTAATTCACCTCC
GGAGCATCTCAAGCTAAAAGGGGAGAGAGTTGGCAGCTAAGTACAATATTCCTTCTATAGAAACAAATGCCAAAGACCCA
CCACTGAATGTTTGCAAAGTGTTCTTTAACCTGGTGAGGTTTAATCAGGCATGAGTCCTCAAAAGGAAGTCAGGGCGAAA
AGATTACCAAACAGCATAGCAAGAAGGCAGTAGAGTTCCAGAAATTAAAGTGCGCCATCTTC

Alignment

ORF - retro_lcha_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATGDIESEYITTYNVVVVGDAFVGKSALAIQFSHDVFVSDLDPTIEDSYVKRAEIDGQVAIINVLDTAG
          MATG..ESEY.TTYNVV.VGDA.VGKSAL.IQFS...F.S.L.PT..DSY.KRAEIDGQVAII.VLD.AG
Retrocopy MATGGSESEYFTTYNVVLVGDANVGKSALGIQFSYGFFISELHPTVTDSYMKRAEIDGQVAIIDVLDAAG

Parental  LEEFSALQDQYLRTGEGFLLVYSVTDEKSFQRVQRLHELILRMKDRDSFPMILVANKVDLIHLRNISSKQ
          LEEFSALQD.YLRTGEGFLLVYSVTDEKSFQ.VQ.LHELILR.KDRDSFPMILVANKVDLIHLR.ISS..
Retrocopy LEEFSALQDWYLRTGEGFLLVYSVTDEKSFQQVQWLHELILRTKDRDSFPMILVANKVDLIHLRSISS*K

Parental  GRELAAKYNIPYVETSAKDPPLNVCKVFFDLVR-LIRHESSKGSQGEKITKQHSDKAVDFQKLKCTIF
          GRELAAKYNIP..ET.AKDPPLNVCKVFF.LVR.LIRHESSKGSQGEKITKQHS.KAV.FQKLKC.IF
Retrocopy GRELAAKYNIPSIETNAKDPPLNVCKVFFNLVR>LIRHESSKGSQGEKITKQHSKKAVEFQKLKCAIF

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	0.00 RPM	0.00 RPM
DRP000627_kidney	0.16 RPM	0.00 RPM
DRP000627_pectoral_fin	0.00 RPM	0.00 RPM
DRP000627_pelvic_fin	0.00 RPM	0.00 RPM
DRP000627_pharynx	0.05 RPM	0.03 RPM
DRP000627_tail_muscle	0.00 RPM	0.02 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_123 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
Bos taurus	ENSBTAG00000001497	1 retrocopy	retro_btau_1032,
Latimeria chalumnae	ENSLACG00000016958	1 retrocopy	retro_lcha_123 ,