RetrogeneDB ID: retro_acar_22

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL344177.1:49645..51184(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000023181
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000026996
• Aliases: None
• Description: None

Sequence

>retro_acar_22
TTAAATATACATAACACTGCTGACATGGAGGAGAAAGCATATAAATGTATCGATTGTGGAAAGAGCTTTAGTCAGCATGG
AAAGCTGAAGACACATCAAAGGATTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTCGCTGATA
GTTCAGGCCTACGTTCCCATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCT
CATAGTTCAGGACTACGTTCCCATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAATGTGAACAGACCTT
CGCTCAGATTTCAACTTTACATTCACATCAAAGAACTCACACTGGGGAGAAACCCTTTAAATGCCTGGAGTGTGGACAGA
GCTGCACTCACAGTTCAGACTTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGA
CAGAGCTTCGCTCAAAGTGGAAACCTAAGTTCACATCAAAGGACCCACACAGGGGAGAAACCCTATAAATGCCTGGAGTG
TGGACAGAGCTTCGCTCGTAGTTCAGGTCTACGTTCACATCATAGGACTCACACTAGGGAGAAACCCAATAACTGTCTGG
AGTGTGGAAAGAGCTTTGCTCATAGTTCAGGGCTACGTTTACATCAAAGGACTCACACTGGGGAGAAGCCCTATGAATGC
TTGGAGTGTGGACAGAGCTTCAGTGATTGTTCAACTCTACGTAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAA
CTGCCTGGAGTGTGGACAGAGCTTTGCTCATAGTTCAGGACTACGTTCCCATCAAAGGACTCACACTGGGGAGAAACCCT
ATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCATAGTTCAGGACTACGTTCCCATCTAAGGACTCACACTGGGGAGAAA
CCCTATAAATGCTTGGAGTGTGGACAGAGCTTCGCTCGTAGGGGAAATCTAGTTTCACATCAAAAGACTCACACAGGGGA
GAAACCCTATAACTGCTTGGAGTGTGGACAGAGCTTTACACAGAAGGGAAACTTACGTTCCCATCAAAGGACTCACACTG
GGGAGAAACCCTATGAATGCCTGGAATGTGAACAGACCTTCGCTCAGATTGCAACTTTACATTCACATCAAAGAACTCAC
ACTGGGGAGAAACCCTATAAATGCCTGGAATGTGAACAGACCTTCGCTCAGATTGCAACTTTACATTCACATCAAAGAAC
TCACACTGGGGAGAAACCCTTTAGATGCCTGGAGTGTGGACTGAGCTTCACTCACAATTCAGAGTTACGTTCACATCAAA
GGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCGCTCAAAGTGGAAACCTAAGTTCACAT
CAAAGGACCCACACTGGGGAGAAACCCTATAAATGTCTGGAGTGTGGACAGAGCTTCGCTCGTAGTTCAGGTCTACGTTC
ACATCATAGGACTCACATG

Alignment

ORF - retro_acar_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.79 %
• Parental protein coverage: 84.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPYNCLECGQSFADSSGLRSHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTGEKPYKCLECEQTFA
          EKPYNCLECGQSFADSSGLRSHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTGEKPYKCLECEQTFA
Retrocopy EKPYNCLECGQSFADSSGLRSHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTGEKPYKCLECEQTFA

Parental  QISTLHSHQRTHTGEKPFKCLECGQSCTHSSDLRSHQRTHTGEKPYKCLECGQSFAQSGNLSSHQRTHTG
          QISTLHSHQRTHTGEKPFKCLECGQSCTHSSDLRSHQRTHTGEKPYKCLECGQSFAQSGNLSSHQRTHTG
Retrocopy QISTLHSHQRTHTGEKPFKCLECGQSCTHSSDLRSHQRTHTGEKPYKCLECGQSFAQSGNLSSHQRTHTG

Parental  EKPYKCLECGQSFARSSGLRSHHRTHTREKPNNCLECGKSFAHSSGLRLHQRTHTGEKPYECLECGQSFS
          EKPYKCLECGQSFARSSGLRSHHRTHTREKPNNCLECGKSFAHSSGLRLHQRTHTGEKPYECLECGQSFS
Retrocopy EKPYKCLECGQSFARSSGLRSHHRTHTREKPNNCLECGKSFAHSSGLRLHQRTHTGEKPYECLECGQSFS

Parental  DCSTLRRHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTGEKPYNCLECGQSFAHSSGLRSHLRTHTG
          DCSTLRRHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTGEKPYNCLECGQSFAHSSGLRSHLRTHTG
Retrocopy DCSTLRRHQRTHTGEKPYNCLECGQSFAHSSGLRSHQRTHTGEKPYNCLECGQSFAHSSGLRSHLRTHTG

Parental  EKPYKCLECGQSFARRGNLVSHQKRTHTGEKPFRCLECGLSFTHNSELRSHQRTHTGEKPYKCLECGQSF
          EKPYKCLECGQSFARRGNLVSHQK.THTGEKP..CLECG.SFT....LRSHQRTHTGEKPY.CLEC.Q.F
Retrocopy EKPYKCLECGQSFARRGNLVSHQK-THTGEKPYNCLECGQSFTQKGNLRSHQRTHTGEKPYECLECEQTF

Parental  AQSGNLSSHQRTHTGEKPYKCLECGQSFARSSTLHAHQRTHTGEKPYNCLQCGQSFTHSSSLRRHQRTHT
          AQ...L.SHQRTHTGEKPYKCLEC.Q.FA...TLH.HQRTHTGEKP..CL.CG.SFTH.S.LR.HQRTHT
Retrocopy AQIATLHSHQRTHTGEKPYKCLECEQTFAQIATLHSHQRTHTGEKPFRCLECGLSFTHNSELRSHQRTHT

Parental  GEKPFKCLECGQSFTQSSGLRSHQRTHTGEKPFKCLECGQSFTYSSCLRKHQRTH
          GEKP.KCLECGQSF.QS..L.SHQRTHTGEKP.KCLECGQSF..SS.LR.H.RTH
Retrocopy GEKPYKCLECGQSFAQSGNLSSHQRTHTGEKPYKCLECGQSFARSSGLRSHHRTH

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	0.56 RPM	0.16 RPM
SRP009831_brain	1.33 RPM	0.33 RPM
SRP009831_dewlap	3.84 RPM	2.15 RPM
SRP009831_embryo	1.84 RPM	0.33 RPM
SRP009831_heart	0.88 RPM	0.42 RPM
SRP009831_liver	0.20 RPM	0.00 RPM
SRP009831_lung	0.25 RPM	0.10 RPM
SRP009831_ovary	3.13 RPM	0.77 RPM
SRP009831_skeletal_muscle	0.07 RPM	0.07 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_22 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_22 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22 ,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248,