RetrogeneDB ID: retro_acar_48

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:69780141..69780840(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000006758
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDHD1
• Ensembl ID: ENSACAG00000004616
• Aliases: None
• Description: haloacid dehalogenase-like hydrolase domain containing 1 [Source:HGNC Symbol;Acc:16818]

Sequence

>retro_acar_48
ATGACAGCCTGTGTTTGTAAGCCCCAGCAGCCCATCACGCATGTCATTTTTGACCTGGATGGCACCCTTTTGAACACCGA
GACCCTCTACACAGCGGTGCTGGAAGAAGTCTGCAGCCGCCATGGGAAGAAATTCACTTGGGAGCAGAAAGAGGTCATCA
TGGGCAGAAGAGAATTGGAGGGTCTAGATATGCTTCGGAAGATCCTTAACATCCCCTTGACGGCTGAGCAAATGATTCAA
GAAGCTGACAAGAAAAAGAAAGAATTGTTTCCCACTGCTCAGCTCATGCCTGGAGCCGAAAGGCTGGTCCACCATCTACA
CCGGCACAAGATCCCCATTGCGGTGGGCTCCAGCTCCCTCCGAGAGCCATACGAATTGAAAACTGGCCACCACAAGGCCT
TCTTTGGCTTGTTCCATCACATCACGTTGGGAGACGATCCGGAAGTGAAAAATGGAAAGCCGCACCCAGATATTTTCCTG
ATCTGCGCCAAAAGATTTGACCCTCCAGCGTCTCCGGCCAAGTGCCTCGTATTTGAAGATGCTCCCAATGGGGTCAAAGC
TGCCAAAGAGGCTGGGATGCAAGTGATCATGATTCCCGATGAACACCTGAATAAAGAGCTCACTAAAGAAGCCACTTTGG
TCCTCCAGTCTATGAAGGACTTCAAGCCAGAAATGTTCGGCCTACCAAAACTTGACTGA

Alignment

ORF - retro_acar_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.46 %
• Parental protein coverage: 96.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PLPRVLMGITAFSSDTERLYTVVYQEICKRYGKSYTWDVKSLAMGKKALEGAKIIRDALDLPLTKEELLH
          P...V..........TE.LYT.V..E.C.R.GK..TW..K...MG...LEG....R..L..PLT.E....
Retrocopy PITHVIFDLDGTLLNTETLYTAVLEEVCSRHGKKFTWEQKEVIMGRRELEGLDMLRKILNIPLTAEQMIQ

Parental  ECQIKQEKLFPTAALMPGVEKLIRHLHQHNIPIAVATSSSRVTFEMKTSRHKDFFNLFHHIVLGDDPEVK
          E...K...LFPTA.LMPG.E.L..HLH.H.IPIAV..SS.R...E.KT..HK.FF.LFHHI.LGDDPEVK
Retrocopy EADKKKKELFPTAQLMPGAERLVHHLHRHKIPIAVGSSSLREPYELKTGHHKAFFGLFHHITLGDDPEVK

Parental  DGKPQPDVFIVCAKRFNPP
          .GKP.PD.F..CAKRF.PP
Retrocopy NGKPHPDIFLICAKRFDPP

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
SRP009831_adrenal	0.13 RPM	2.33 RPM
SRP009831_brain	0.00 RPM	2.98 RPM
SRP009831_dewlap	0.08 RPM	22.74 RPM
SRP009831_embryo	0.00 RPM	8.06 RPM
SRP009831_heart	0.26 RPM	5.81 RPM
SRP009831_liver	0.00 RPM	3.15 RPM
SRP009831_lung	0.00 RPM	5.19 RPM
SRP009831_ovary	0.08 RPM	28.57 RPM
SRP009831_skeletal_muscle	0.00 RPM	7.18 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_48 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_48 was not experimentally validated.

Homology

Retrocopy orthology:

Anolis carolinensis 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004616	1 retrocopy	retro_acar_48 ,
Choloepus hoffmanni	ENSCHOG00000001318	5 retrocopies	retro_chof_1597, retro_chof_1855, retro_chof_1883, retro_chof_2136, retro_chof_2168,
Homo sapiens	ENSG00000130021	2 retrocopies	retro_hsap_2469, retro_hsap_454,
Gorilla gorilla	ENSGGOG00000004425	1 retrocopy	retro_ggor_1537,
Microcebus murinus	ENSMICG00000017082	1 retrocopy	retro_mmur_1321,
Macaca mulatta	ENSMMUG00000017377	1 retrocopy	retro_mmul_244,
Monodelphis domestica	ENSMODG00000017505	2 retrocopies	retro_mdom_1374, retro_mdom_52,
Pongo abelii	ENSPPYG00000020105	2 retrocopies	retro_pabe_1837, retro_pabe_280,
Pteropus vampyrus	ENSPVAG00000011149	1 retrocopy	retro_pvam_1165,
Tarsius syrichta	ENSTSYG00000013238	4 retrocopies	retro_tsyr_2013, retro_tsyr_345, retro_tsyr_542, retro_tsyr_931,