RetrogeneDB ID: retro_acar_96

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:75410675..75411056(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000004589
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5D
• Ensembl ID: ENSACAG00000002168
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit [Source:HGNC Symbol;Acc:837]

Sequence

>retro_acar_96
CCTTCACCATCACCTCGCCCTTGCAGGTTTTCTACAATGTGGCCCACGTGAAGAAGGTGGATGTCCCTATGCTCAATGGG
GCTTTTTGCATCTTGGCCGCCCATGTCTCGACCCTGCAAGTCCTGAGACCTGGTGTGGTGACCATCTTTGCTGAGGACAG
GGCCTCCACAAAGTACTTCATCAGCAGTGGATCCATCACAGTGAACATGGACTCCTCCGTCCAGCTCCTAAGTTACGCTC
TTGGATCTACTCGATCTGATGGCAGCCAAATCTAACCTGGAGAAGGCCTTGTCGGAGATGGCCACTGGTTCTGATGAATC
TGCCAAGGCAGAGGCCCAGATACGCGTGGAGGCCAATGAAGCCCTAGTGAAGGTGCTAGAG

Alignment

ORF - retro_acar_96 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 78.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PNPQPQSC-WVFYNAAHVKQVDVPTLSGAFGILAAHVPTLQVLRPGVVTVFAEDGASTKYFVSSGSVTVN
          P.P.P..C..VFYN.AHVK.VDVP.L.GAF.ILAAHV.TLQVLRPGVVT.FAED.ASTKYF.SSGS.TVN
Retrocopy PSPSPRPC<QVFYNVAHVKKVDVPMLNGAFCILAAHVSTLQVLRPGVVTIFAEDRASTKYFISSGSITVN

Parental  ADSSVQLLAEEVA-LLDQLDLAAAKSNLEKALSEMAAASDESAKAEAQIRVEANEALVKALE
          .DSSVQLL......LLD...L.AAKSNLEKALSEMA..SDESAKAEAQIRVEANEALVK.LE
Retrocopy MDSSVQLLSYALG>LLD---LMAAKSNLEKALSEMATGSDESAKAEAQIRVEANEALVKVLE

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	0.00 RPM	43.88 RPM
SRP009831_brain	0.00 RPM	52.22 RPM
SRP009831_dewlap	0.00 RPM	28.60 RPM
SRP009831_embryo	0.00 RPM	59.01 RPM
SRP009831_heart	0.00 RPM	210.28 RPM
SRP009831_liver	0.00 RPM	55.87 RPM
SRP009831_lung	0.00 RPM	39.14 RPM
SRP009831_ovary	0.04 RPM	32.70 RPM
SRP009831_skeletal_muscle	0.00 RPM	89.63 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_96 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_96 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002168	1 retrocopy	retro_acar_96 ,
Canis familiaris	ENSCAFG00000019536	1 retrocopy	retro_cfam_1372,
Microcebus murinus	ENSMICG00000014960	1 retrocopy	retro_mmur_1137,
Myotis lucifugus	ENSMLUG00000015004	1 retrocopy	retro_mluc_2544,
Monodelphis domestica	ENSMODG00000005314	1 retrocopy	retro_mdom_1079,
Rattus norvegicus	ENSRNOG00000014625	1 retrocopy	retro_rnor_1978,