RetrogeneDB ID: retro_acar_151

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: AAWZ02040337:6184..6531(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1AY
• Ensembl ID: ENSACAG00000012660
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, Y-linked [Source:HGNC Symbol;Acc:3252]

Sequence

>retro_acar_151
GAAGAAGATGGACAAGAATCTGCTCAAGTTATCAAAACGCTGGGGAATGGTAGATTGGAAGCATTAGATTTTGCTGGTGT
AAAGAGGTTACGCCACATCAGAGGAAAACCGAGGGAAAAGGTTTGGATAAATACATCAGATATCATATTGGTGGGTTTGT
GAGACTACCAGGGGAACAAGGCTGATGTAATTTGAAGTACAAGGCAGAGGCAGGCAGAAGTCTGAAGACACATGGGGAAC
TCCCCCCACATGCCAGATTTAATGAAAGGGATACATTTGGGCCTGGAGATGATGACAAAATCGGGTCTGATGACCTTGGG
GATGATGATGACGACACTGATGATATC

Alignment

ORF - retro_acar_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.92 %
• Parental protein coverage: 80.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEDGQEYAQVIKMLGNGRLEALCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRDYQDNKADVI-LKYNA
          .EDGQE.AQVIK.LGNGRLEAL.F.GVKRL.HIRGK.R.KVWINTSDIILVGL.DYQ.NKADVI.LKY.A
Retrocopy EEDGQESAQVIKTLGNGRLEALDFAGVKRLRHIRGKPREKVWINTSDIILVGL*DYQGNKADVI<LKYKA

Parental  DEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDEDIDDI
          ...RSLK..GELP.HA..NE.DTFGPGDDD.I..DD.GDDD.D.DDI
Retrocopy EAGRSLKTHGELPPHARFNERDTFGPGDDDKIGSDDLGDDDDDTDDI

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	0.16 RPM	136.64 RPM
SRP009831_brain	0.09 RPM	138.28 RPM
SRP009831_dewlap	0.00 RPM	107.58 RPM
SRP009831_embryo	0.18 RPM	139.06 RPM
SRP009831_heart	0.21 RPM	114.40 RPM
SRP009831_liver	0.08 RPM	101.52 RPM
SRP009831_lung	1.01 RPM	104.22 RPM
SRP009831_ovary	0.08 RPM	93.24 RPM
SRP009831_skeletal_muscle	0.00 RPM	111.78 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_151 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_151 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012660	1 retrocopy	retro_acar_151 ,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,