RetrogeneDB ID: retro_acar_50

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL344727.1:7565..9014(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000017749
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000022348
• Aliases: None
• Description: None

Sequence

>retro_acar_50
ATGAAGGAGAAAGCGTATAAATGCCTGGAGTGTGGAAAGAGTTTCACGCAGAGGGGTCATCTGTGGCAACATGACAAGAT
TCACACTGGGAAGAAGCCCTATAAATGCCTGGAGTGTGGACAGAGTTTCACTCGGAGTGGAAGTCTACGTACACATCAAA
GGACTCACACTGGGGAAAAACCCTACACATGCCTGGAGTGTGGAAGAAGCTTCAGTCATAGTTCAGGTCTGTGTAGACAT
CAAAAGACTCACACTGGGGAGAGACCTTATGAATGCCTGGAGTGTGGGCAGAGCTTCACTCGGAGTGACATTCTACATTC
ACATCAAAGGATTCACACTGGGGAGAAACCTTATACATGCCCCGAATGCGGTCAGAACTTCACTAAGAATTCGGATCTAT
ATAGTCATCAGAAGACTCACACTGGGGAGAAACCCTACACATGCCTGGAGTGTGGAAGAAGCTTCCGTCATAGTTCAAAT
CTGTATTCACATCAAAGGACTCACACTGGGGAGAAGCCCTATGAATGCCTGGAGTGTGGACAGAGCTTCACTCAGAGTGG
ACATCTACGTGTACATCAAAGGACTCACACTGGGGAGAAACCTTATACATGCCTGGAGTGTGGACAGAAGTTCACTGAGA
GTTCAGCTATACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTACAAATGCCTGGAGTGTGGAAAAAGCTTCACT
ACCAATTCAGGTCTACGTTCACATCAGAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAAAGCTT
CACTCAGATTGAAACTCTACGTTCACATCAAAGGACTCACACTGGGGAGAAGCCCTATGAATGCCTGGAGTGTGGACAGA
GCTTCACTCAGAGTGGACATCTACGTATACATCAAAGGACTCACACTGGGGAGAAACCCTACAAATGCCTGGAGTGTGGA
AAAAGCTTCACTACCAATTCAGGTCTACATTCACATCAGAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTG
CGGACAAAGCTTCGCTCATAATCAGCGTCTACGTTCACATCAGAGGACTCACAGTGGGGAGAAACCTTATGAATGCCATG
AATGTGGACAGAGCTACTCTCGGATTGAAAGTCTACGTTCACATCAAAGCACTCACACTGGGAAGAAACCCTATAAATGC
CTGGAGTGTGGAAAAAGCTTCGCTCAGAGTTCACATCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTACAA
ATGCCTGGAGTGTGGAAAAAGCTTCGCTCATAGTTCACGTCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCTT
ATAAATGCCTGGAGTGTGAACAGAGCTTCACTCGGCTTGAAAGTCTACATTCACATCAGAGGACTCACACTGGGGAGAAA
CCCTATGAA

Alignment

ORF - retro_acar_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.88 %
• Parental protein coverage: 53.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPYKCLECGQSFSHNSHLHRHQRTHTGEKPYICLECGQSFARSSSLRSHQRTHTGEKPYKCLECGQSFA
          EK.YKCLECG.SF....HL..H...HTG.KPY.CLECGQSF.RS.SLR.HQRTHTGEKPY.CLECG.SF.
Retrocopy EKAYKCLECGKSFTQRGHLWQHDKIHTGKKPYKCLECGQSFTRSGSLRTHQRTHTGEKPYTCLECGRSFS

Parental  HSSALHRHQRTHTGEKTYHCLECGQSFAHSSALHRHQRTHTGEKPYHCLECGQSFTDRSGLRSHQRTHTG
          HSS.L.RHQ.THTGE..Y.CLECGQSF..S..LH.HQR.HTGEKPY.C.ECGQ.FT..S.L.SHQ.THTG
Retrocopy HSSGLCRHQKTHTGERPYECLECGQSFTRSDILHSHQRIHTGEKPYTCPECGQNFTKNSDLYSHQKTHTG

Parental  EKPYICLECGQSFARSSGLRSHQRTHTGEKPYECLECGQSFTHNSGLRSHQRTHTGEKPYKCLECGQSFS
          EKPY.CLECG.SF..SS.L.SHQRTHTGEKPYECLECGQSFT....LR.HQRTHTGEKPY.CLECGQ.F.
Retrocopy EKPYTCLECGRSFRHSSNLYSHQRTHTGEKPYECLECGQSFTQSGHLRVHQRTHTGEKPYTCLECGQKFT

Parental  RSSVLRSHERTHTGEKPYECLECGQSFSDCSTLRKHQRIHTGEKPYKCVECGQSFTRKGRLRSHQRTHTG
          .SS..RSH.RTHTGEKPY.CLECG.SF...S.LR.HQR.HTGEKPYKC.ECGQSFT....LRSHQRTHTG
Retrocopy ESSAIRSHQRTHTGEKPYKCLECGKSFTTNSGLRSHQRTHTGEKPYKCLECGQSFTQIETLRSHQRTHTG

Parental  EKPYKCLECGQSFTQSSGLRIHQRTHTGEKPYKCLECGQTFTHNSGLRSHQRTHTGEKPYNCLECGQSFT
          EKPY.CLECGQSFTQS..LRIHQRTHTGEKPYKCLECG..FT.NSGL.SHQRTHTGEKPY.CLECGQSF.
Retrocopy EKPYECLECGQSFTQSGHLRIHQRTHTGEKPYKCLECGKSFTTNSGLHSHQRTHTGEKPYKCLECGQSFA

Parental  HNSDLRSHQRTHTGEKPYKCLECGQSFTRNSGLRSHHRTHTGEKPYECLECGQSFSDCSTLRKHQRTHTG
          HN..LRSHQRTH.GEKPY.C.ECGQS..R...LRSH..THTG.KPY.CLECG.SF...S.LR.HQRTHTG
Retrocopy HNQRLRSHQRTHSGEKPYECHECGQSYSRIESLRSHQSTHTGKKPYKCLECGKSFAQSSHLRSHQRTHTG

Parental  EKPYKCVECGQSFTRKGHLHSHQRTHTGEKPYDCLECGQSFAQSSTLHIHQRTHTGEKPYK
          EKPYKC.ECG.SF.....L.SHQRTHTGEKPY.CLEC.QSF.....LH.HQRTHTGEKPY.
Retrocopy EKPYKCLECGKSFAHSSRLRSHQRTHTGEKPYKCLECEQSFTRLESLHSHQRTHTGEKPYE

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	16.51 RPM	23.14 RPM
SRP009831_brain	8.33 RPM	5.92 RPM
SRP009831_dewlap	1.01 RPM	6.58 RPM
SRP009831_embryo	11.20 RPM	9.60 RPM
SRP009831_heart	7.94 RPM	12.87 RPM
SRP009831_liver	4.46 RPM	4.62 RPM
SRP009831_lung	7.00 RPM	10.88 RPM
SRP009831_ovary	0.27 RPM	18.34 RPM
SRP009831_skeletal_muscle	1.68 RPM	1.82 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_50 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_50 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000022348	1 retrocopy	retro_acar_50 ,
Anolis carolinensis	ENSACAG00000024100	1 retrocopy	retro_acar_28,
Anolis carolinensis	ENSACAG00000024147	1 retrocopy	retro_acar_46,
Danio rerio	ENSDARG00000089344	1 retrocopy	retro_drer_10,
Xenopus tropicalis	ENSXETG00000024377	1 retrocopy	retro_xtro_31,