RetrogeneDB ID: retro_acar_30

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343588.1:147295..147856(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000001267
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000001891
• Aliases: None
• Description: None

Sequence

>retro_acar_30
TTGGGGGCCAAGATGTTGGTGTTAGTGTTGGGAGACCTTCATATCCCTCACCGCTGCAACAGTTTGCCAGCAAAGTTCAA
AAAACTTCTGTTTCCAGGGAAGATCCAACACATTCTCTGCACTGGAAACCACTGCACAAAGGAGAGTTATGACTATCTCA
AGACCCTGGCTGGTGATGTTCATGTGGTTAGAGGGGACTTTGATGAGAACTTGAACTACCCTGAACAGAAAGTTGTCACT
GTCGGGCAGTTTAAGATTGGCCTGATCCACGGCCAGCAAGTGATCCCATGGGGAGACGTGGCCAGCCTGGCGCTGCTCCA
GAGACAGTTTGATGTGGACATCCTGATTTCTGGGCACACACACAAATTTGAGGCCTTTGAGCATGAAAACAAGTTCTATA
TCAATCCTGGATCAGCAACAGGAGTGTACAGTGCTTTGGAAAACAACATCATACCTTCTTTTGTACCGATGGATATCCAA
GCTTCCACCATCATGACCTATGTTTATCAGCTAATTGGCGACAACGTCAAGGTAGAAAGAATTGAGTACAAGAAATCTTA
A

Alignment

ORF - retro_acar_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.58 %
• Parental protein coverage: 97.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHVVRGDFDENLNYPE
          LVLVLGDLHIPHRCNSLPAKFKKLL.PGKIQHILCTGN.CTKESYDYLKTLAGDVHVVRGDFDENLNYPE
Retrocopy LVLVLGDLHIPHRCNSLPAKFKKLLFPGKIQHILCTGNHCTKESYDYLKTLAGDVHVVRGDFDENLNYPE

Parental  QKVVTVGQFKIGLIHGHQVIPWGDVASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYSA
          QKVVTVGQFKIGLIHG.QVIPWGDVASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATG.YSA
Retrocopy QKVVTVGQFKIGLIHGQQVIPWGDVASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGVYSA

Parental  LENNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS
          LENNIIPSFV.MDIQAST..TYVYQLIGD.VKVERIEYKKS
Retrocopy LENNIIPSFVPMDIQASTIMTYVYQLIGDNVKVERIEYKKS

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	4.17 RPM	154.59 RPM
SRP009831_brain	0.28 RPM	115.75 RPM
SRP009831_dewlap	0.25 RPM	53.91 RPM
SRP009831_embryo	2.64 RPM	85.03 RPM
SRP009831_heart	0.10 RPM	61.58 RPM
SRP009831_liver	0.16 RPM	51.45 RPM
SRP009831_lung	0.25 RPM	31.68 RPM
SRP009831_ovary	0.12 RPM	47.41 RPM
SRP009831_skeletal_muscle	0.11 RPM	15.44 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_30 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_30 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 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30 ,
Felis catus	ENSFCAG00000004135	2 retrocopies	retro_fcat_165, retro_fcat_848,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115,
Monodelphis domestica	ENSMODG00000011577	1 retrocopy	retro_mdom_450,
Oryctolagus cuniculus	ENSOCUG00000011924	1 retrocopy	retro_ocun_1611,
Procavia capensis	ENSPCAG00000012049	1 retrocopy	retro_pcap_158,
Tupaia belangeri	ENSTBEG00000012756	4 retrocopies	retro_tbel_1121, retro_tbel_2187, retro_tbel_330, retro_tbel_4424,
Tursiops truncatus	ENSTTRG00000015090	2 retrocopies	retro_ttru_1404, retro_ttru_1492,