RetrogeneDB ID: retro_acar_184

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343389.1:547040..547628(+)
• Located in intron of: ENSACAG00000005252

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSACAG00000010365
• Aliases: None
• Description: None

Sequence

>retro_acar_184
GGAAGGTATGGTGGCTTTGATGAGTATGGTGGCTATAACAATTATGGCTATGGAAATGATGGCTATGATGACAGAATGAG
AGATGGGAGAGGAATGGGAGGCCATGGGTATGGTGGAGCAGGAGATGCCAGCTCAGGCTTTCAAGGTGGTCATTTTGTTC
ACATGAGGGGATTGCCATTTCGAGCTACAGAAAATAACATAGCTAATTTTTTTTCACCACTGACCCCTATAAGAGTTCAT
ATTGACATTGGAGCAGACGGTAGAGCAACAGGCGAAGCTGATGTAGAATTTGTGACACACGAAGATGCAGTGGCTGCCAT
GTCAAAGGATAAAAATCATATGCAACATCGATACATTGAGTTGTTCCTGAATTCAACTGCTGGAGGCGGTGCTGGCATGG
GAGGCTATGGCAGAGATGGCATGGATCAAGGTGGTTATGGTTCCGTAGAAAGAATGGGAATGGGCAGCAGTTACAGTGGA
GGATATGGTACTCCCGATGGATTAGGTGGCTATGGTCGTGGCAGTGGAAATAGTGGTGGATACTATGGTAAAGGCAACAT
GGGAGGAGGTGGATGGCGTGGAATGTAT

Alignment

ORF - retro_acar_184 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.45 %
• Parental protein coverage: 57.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGYGGFDEYGGYNNYGYGNDGYDDRMRDGRGMGGHGYGGAGDASSGFQGGHFVHMRGLPFRATENDIANF
          G.YGGFDEYGGYNNYGYGNDGYDDRMRDGRGMGGHGYGGAGDASSGFQGGHFVHMRGLPFRATEN.IANF
Retrocopy GRYGGFDEYGGYNNYGYGNDGYDDRMRDGRGMGGHGYGGAGDASSGFQGGHFVHMRGLPFRATENNIANF

Parental  FSPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQHRYIELFLNSTAGGGAGMGGYGRDG
          FSPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQHRYIELFLNSTAGGGAGMGGYGRDG
Retrocopy FSPLTPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQHRYIELFLNSTAGGGAGMGGYGRDG

Parental  MDQGGYGSVGRMGMGSSYSGGYGTPDGLGGYGRGSGNSGGYYGQGNMGGAGWRGMY
          MDQGGYGSV.RMGMGSSYSGGYGTPDGLGGYGRGSGNSGGYYG.GNMGG.GWRGMY
Retrocopy MDQGGYGSVERMGMGSSYSGGYGTPDGLGGYGRGSGNSGGYYGKGNMGGGGWRGMY

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	5.84 RPM	129.42 RPM
SRP009831_brain	0.95 RPM	89.66 RPM
SRP009831_dewlap	1.27 RPM	73.66 RPM
SRP009831_embryo	11.20 RPM	305.90 RPM
SRP009831_heart	1.92 RPM	149.32 RPM
SRP009831_liver	0.70 RPM	44.05 RPM
SRP009831_lung	0.91 RPM	96.26 RPM
SRP009831_ovary	0.73 RPM	69.15 RPM
SRP009831_skeletal_muscle	0.44 RPM	20.98 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_184 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_184 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184 ,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,