RetrogeneDB ID: retro_acar_29

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL344166.1:40911..42558(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000029118
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000027062
• Aliases: None
• Description: None

Sequence

>retro_acar_29
ATGAAGGAGGAAGCATCTAAAAACCTGGAGTGTGGAAAGAGTTACACTCAGAATTATGGTCTGCAGCGACATGAAAGGAC
ACACACTGGGGAGAAACCCTATAAATGCCTAGAGTGTGGAAAGAGCTTTGCTCAGAGTGGAGATCTACGTAAACATCAAA
GGACTCACACTGGGGAGAAACCTTATACATGCCTGGAGTGCGGAAAGAGCTTCACTCAGAGAGTACATCTAGATTCACAT
CAAAGGACTCACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAGCTTCACTCAGAGTTCAAATCTAGGTTC
TCATCAGCGGACTCACACTGGGGAAAAACCTTATCCATGCCTGGAGTGTGGAAAGAGCTTTACTCAGAGTTCACAGCTAC
GTTTGCATCAAAGGACTCACACCGGGGAGAAACCCCATACATGCCTGGAATGTCGACACAGCTTCAATCGGATTTCAGAT
CTACGTTTACATCAAAGAACTCACACTGGAGAAAAACCTTATGCATGCCTGGAGTGTGGAAAGAGTTTTACTAAGAGTTC
AAAACTACGTTTGCATCAAAGGACTCACACTGGGGAGAAACCCTATATGTGTCTGGAATGTGGACAGAGCTTCACTCAGA
GTTCAAGTCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCTTACACATGCCTGGAGTGCGGAAAGAGCTTTACT
TTTAGTTCAAGTCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCTTATACATGCCTGGAGTGCGGAAAGAGCTT
TACTAAGAGTTCAGATCTACGTTTGCATGAAAGGACCCACACTGGGGAAAAACCTTATACATGCCTGGAGTGCGGAAAGA
GCTTTACTAAGAGTTCAGATCTACGATCACATCAACGGACCCACACTGGGGAAAAACCTTATACATGCCTGGAGTGCGGA
AAGAGCTTTATTAAGAGTTCAGGTCTACGATCACATCAATGGACTCACACTGGGGATAAACCTTATACATGCCTGGAGTG
TGGAAAGAGCTTTACTAAGAGTTCAAATCTATGTAGGCATCAAAGGACTCACACTGGGGAGAAACCTTATACATGCCTGG
AGTGTGGGCAGAGATTCACTAACAGTTCAAGTCTACGTGCACATCAGTGGACTCACACTGGGGAGAAACCCTATACATGC
CTGGTGTGTGGACAGAGATTCACTAACAGTTCAAGTCTACGTTCACATCAAAGGAATCACTCTGGGGAGAAACCTTATAC
ATGCCTGGAGTGTGGACAGAGATTCACTAACAGTTCAAGTCTACGTTCACATCAATGGATTCACACTGGGGAAAAACCTT
ATACATGCCTGGAGTGCAGAAAGAGCTTTACTCAGAGTTCAAATCTACGTAGGCATCAGCGGACTCACACTGGGGAGAAA
CCCTACACATGCCTGGAGTGTGGACGCAACTTTACTGAGAGTGGAGGTCTACATAAACATCAAAGGACTCACGCTGGGGA
GAAACCTTATACATGCCTGGAGTGCAGAAAGAGCTTCACTAAGTGTTCAAATCTATGTTTGCATCAAAGGATTCGCCCTG
GGGAGAAAACCCTATACATGCCAGGAGTATGGACAGAGTTTTGCTGA

Alignment

ORF - retro_acar_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.03 %
• Parental protein coverage: 81.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPFKCLECGQSFTESGSLRTHQRTHTGEKPYTCLECGKSFTERSSLRLHQRTHTGEKPYACLECGKSFA
          E...K.LECG.S.T....L..H.RTHTGEKPY.CLECGKSF.....LR.HQRTHTGEKPY.CLECGKSF.
Retrocopy EEASKNLECGKSYTQNYGLQRHERTHTGEKPYKCLECGKSFAQSGDLRKHQRTHTGEKPYTCLECGKSFT

Parental  QKGHLDSHQRTHTGEKPYTCQECGMSFAQSSNLHSHQRTHTGEKPCKCLVCGQSFTKNSSLRLHEMTHTG
          Q..HLDSHQRTHTGEKPYTC.ECG.SF.QSSNL.SHQRTHTGEKP..CL.CG.SFT..S.LRLH..THTG
Retrocopy QRVHLDSHQRTHTGEKPYTCLECGQSFTQSSNLGSHQRTHTGEKPYPCLECGKSFTQSSQLRLHQRTHTG

Parental  EKPYTCQECGQSFTKNSSLRLHEMTHTGEKPYTCQECGQSFTKHSSLRLHQMTHTGEKPYTCQECGKSFT
          EKP.TC.EC..SF...S.LRLH..THTGEKPY.C.ECG.SFTK.S.LRLHQ.THTGEKPY.C.ECG.SFT
Retrocopy EKPHTCLECRHSFNRISDLRLHQRTHTGEKPYACLECGKSFTKSSKLRLHQRTHTGEKPYMCLECGQSFT

Parental  QSSNLYSHQRTHTGEKPCKCLECGQSFTTNSSLRLHQMTHTGEKPYTCQECGKSFTKNSSLRLHQRTHTG
          QSS.L.SHQRTHTGEKP..CLECG.SFT..SSLR.HQ.THTGEKPYTC.ECGKSFTK.S.LRLH.RTHTG
Retrocopy QSSSLRSHQRTHTGEKPYTCLECGKSFTFSSSLRSHQRTHTGEKPYTCLECGKSFTKSSDLRLHERTHTG

Parental  EKPYTCQECGRSFTESSNLRSHQWTHTGEKPYTCLECGMSFAHSSAVRLHQRTHTGEKPYTCLECGQSFT
          EKPYTC.ECG.SFT.SS.LRSHQ.THTGEKPYTCLECG.SF..SS..R.HQ.THTG.KPYTCLECG.SFT
Retrocopy EKPYTCLECGKSFTKSSDLRSHQRTHTGEKPYTCLECGKSFIKSSGLRSHQWTHTGDKPYTCLECGKSFT

Parental  QSSGLRLHKRTHTGEKPYTCQECGRSFTESSKLRSHQWTHTGEKPYTCLECGQGFTKSSRLRSHQRTHTG
          .SS.L..H.RTHTGEKPYTC.ECG..FT.SS.LR.HQWTHTGEKPYTCL.CGQ.FT.SS.LRSHQR.H.G
Retrocopy KSSNLCRHQRTHTGEKPYTCLECGQRFTNSSSLRAHQWTHTGEKPYTCLVCGQRFTNSSSLRSHQRNHSG

Parental  EKPYTCLECGQSFTNSSSLRLHQRTHTGEKPYTCLECGMSFTHSSGLCRHRRTHTGEKPYTCPECGKSFT
          EKPYTCLECGQ.FTNSSSLR.HQ..HTGEKPYTCLEC..SFT.SS.L.RH.RTHTGEKPYTC.ECG..FT
Retrocopy EKPYTCLECGQRFTNSSSLRSHQWIHTGEKPYTCLECRKSFTQSSNLRRHQRTHTGEKPYTCLECGRNFT

Parental  RSAALRLHQRTHTGEKPYTCLECGKSFTQSGKLRLHQRTHTGEK
          .S..L..HQRTH.GEKPYTCLEC.KSFT....L.LHQR...GEK
Retrocopy ESGGLHKHQRTHAGEKPYTCLECRKSFTKCSNLCLHQRIRPGEK

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	3.68 RPM	7.71 RPM
SRP009831_brain	1.56 RPM	5.92 RPM
SRP009831_dewlap	12.11 RPM	2.02 RPM
SRP009831_embryo	7.77 RPM	28.04 RPM
SRP009831_heart	3.32 RPM	8.04 RPM
SRP009831_liver	1.15 RPM	3.68 RPM
SRP009831_lung	2.32 RPM	6.45 RPM
SRP009831_ovary	12.12 RPM	1.89 RPM
SRP009831_skeletal_muscle	0.62 RPM	1.57 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_29 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_29 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,