RetrogeneDB ID: retro_acar_33

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:119865301..119866294(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000002660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSACAG00000012591
• Aliases: None
• Description: nuclear transcription factor Y, gamma [Source:HGNC Symbol;Acc:7806]

Sequence

>retro_acar_33
CATCATGTCCACGGACGGGGCTTTCCGGGAGGCAGTAGCGATGCCCAACAGTGCCTCCAATCCTTCTGGCCTCGGGTCAT
GGAGGAGATTTGGAATTTGACAGTGAAAGACTTCAGAGTTCAAGAACTTCCATTGGCACACATTAAGAAGATAATGAAAC
TAGATGAGGATGTGAAGATGATCAGGGCTGAAGCACCTGTTCTGTTTGCCAAGGCTGCTCAGATATTCATCACGGAATTG
ACATTACAGGCTTGGATTCACACAGAGGACAACAAGCGCAGGACCCTGCAGAGGAATGACATTGCTATGGCGATCACAAA
GTTTGATCAGTTTGACTTTCTCATTGACATTGTTCAACCTCCCAAGCGACAGGAGGAGGTGTGCCAAGCGGTGACCCCGG
CAGAGCCTGTCCAGTATTACTTCACTTTGGCGCAGCAGCCGGCAGCTGTCGAGGTCCAGGGGCAGCAGACTGGGCAGCAG
ACAACCACATCCACGGCGACCATCCAGCTGGGGCAGATCATCATAGCCCAGCCTCAGCAAGGGCAGACCACTCCTGTGAC
CATGCAGGTGGGTGAAAGGCAGCAGGTCCAGATTGTCCAGGCCCAGCCACAAGGGCAGGCCCAGCCAGCACAGAGCGGGA
GCGGACAGACCATGCAGGTCATGCAGCAGATCATTACCAACACAGGCGAAATTGAACAAATACCGGTCCAGCTCAATGCC
AGTCAGCTGCAGTACATCCGCCTGGCCCAGCCTGTCTTCGGCACCCAGGTCGTCCAGGGCCAGATCCAGACACTTGCCGC
CAGCACACAACAGATTACACAGACGGAGGTTCAACAGGGACAACAGCAATTCAGCCAGTTTACAGACGGACAGCAACTGT
ACCAGATCCAGCAAGTGACCATACCTGCTGGTCAGGACATCACCCAACCCATGTTCATCCAGTCGGCCAGTCAGGCAACA
GATGGGCAGTCCCCACAGGTTACAGGAGACTGA

Alignment

ORF - retro_acar_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DELKPPKRQEEVRQAVTPAEPVQYYFTLAQQPAAVQVQGQQTGQQTTTSTATIQPGQIIIAQPQQGQTTP
          D...PPKRQEEV.QAVTPAEPVQYYFTLAQQPAAV.VQGQQTGQQTTTSTATIQ.GQIIIAQPQQGQTTP
Retrocopy DIVQPPKRQEEVCQAVTPAEPVQYYFTLAQQPAAVEVQGQQTGQQTTTSTATIQLGQIIIAQPQQGQTTP

Parental  VTMQVGEGQQVQIVQAQPQGQAQPAQSGSGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGT
          VTMQVGE.QQVQIVQAQPQGQAQPAQSGSGQTMQVMQQIITNTGEI.QIPVQLNA.QLQYIRLAQPV.GT
Retrocopy VTMQVGERQQVQIVQAQPQGQAQPAQSGSGQTMQVMQQIITNTGEIEQIPVQLNASQLQYIRLAQPVFGT

Parental  QVVQGQIQTLAANTQQITQTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDITQPMFIQSASQATDGQSP
          QVVQGQIQTLAA.TQQITQTEVQQGQQQFSQFTDGQQLYQIQQVT.PAGQDITQPMFIQSASQATDGQSP
Retrocopy QVVQGQIQTLAASTQQITQTEVQQGQQQFSQFTDGQQLYQIQQVTIPAGQDITQPMFIQSASQATDGQSP

Parental  QVTGD
          QVTGD
Retrocopy QVTGD

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	0.03 RPM	119.24 RPM
SRP009831_brain	0.05 RPM	70.87 RPM
SRP009831_dewlap	0.00 RPM	91.97 RPM
SRP009831_embryo	0.44 RPM	85.71 RPM
SRP009831_heart	0.00 RPM	113.05 RPM
SRP009831_liver	0.00 RPM	39.63 RPM
SRP009831_lung	0.10 RPM	70.37 RPM
SRP009831_ovary	0.00 RPM	117.83 RPM
SRP009831_skeletal_muscle	0.00 RPM	26.81 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_33 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_33 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33 ,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844,
Nomascus leucogenys	ENSNLEG00000012195	2 retrocopies	retro_nleu_2369, retro_nleu_2850,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,