RetrogeneDB ID: retro_acar_84

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:119038584..119039501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSPRY1
• Ensembl ID: ENSACAG00000006680
• Aliases: None
• Description: None

Sequence

>retro_acar_84
GACCCCATACAGCCCCCTTGACGGGGACAGGGGTCCCATGAACTGAGGAGGAAAAAAAATAACGTGGATGGATTATTACT
GGACATGCTGGCGATCATTTGGACACTCGTTGGCAATAATCAGGAACCTCCTTATTCCATGATGACTTTGCATGAAATGG
CTGAAATAGATGAAGGCTGGCTGGAAGTTGTCCAATCATTAATTAGAGTTATTCCATTAGAAGATCCCCTGGGTCTAGCT
GTTATAACATTACTACTTGATGAGTGTCCATTGCCAATAAAAGATGCATTCCAGAAGTTGACTGAAATATTAAATATAAG
GAGAGCCGTTGCGCACCAGGATGTGTGCCATTCTGCCAAACATTTGAACACCACCGCCATCCTGGGCTGTTTGGCAGAGA
AGCTTGCAGGTCCTGCAAGTGTAGGTTTACTCAGTCAAGGAATCTTGGAATACTTGCTGCAGAGCTTGGAGTTCCAGTCC
CACCCAACAGTAATGCTTTTTGTACTAACAGCCCTGGAAAAGTTTGCACAAACAAGTGAAAATAAAGTGACTGTTTCCCA
GACTTGCATCAGCGACCAACTTGTCTTGTTAGAGAAAGAGATGGATAATCTGGACTACTTAACGCACCAAGTTGGTTTCT
GCACTCAGTGGAGTTTAGGTAATCTGTTTTGAAATATGGCAGGCAGTTTACGTTCAAGGAGGTTGGCTTGACCCACATTA
ATGCCATGCTGAATAGTAACAACATCAGTGAATACCTTCAGATCTCATTGCATGGGTTGAATGTCTGATGCGATGCCTCC
TCTTTTGAAAGCGTCTGGTGTACCTACTGTGTGGATTTTGGAGTCTGATATTATGAAGTCACCATCATCACTTCTGGAGT
GATTTAGATCAGATGGGCTACCAAAGACGGCAATTAT

Alignment

ORF - retro_acar_84 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 52.85 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPVRPPRRGRGPHEPRRKKHNVDGLVLDTLAVIRTLVDNDQEPPYSMMTLHEMAETDEGWLEVVQSLIRV
          DP..PP.RG.G.HE.RRKK.NVDGL.LD.LA.I.TLV.N.QEPPYSMMTLHEMAE.DEGWLEVVQSLIRV
Retrocopy DPIQPP*RGQGSHELRRKKNNVDGLLLDMLAIIWTLVGNNQEPPYSMMTLHEMAEIDEGWLEVVQSLIRV

Parental  IPLEDPLGPAVITLLLDECPLPTKDALQKLTEILNLSGAVARQDACHPAKHRNTTAVLGCLAEKLAGPAS
          IPLEDPLG.AVITLLLDECPLP.KDA.QKLTEILN...AVA.QD.CH.AKH.NTTA.LGCLAEKLAGPAS
Retrocopy IPLEDPLGLAVITLLLDECPLPIKDAFQKLTEILNIRRAVAHQDVCHSAKHLNTTAILGCLAEKLAGPAS

Parental  IGLLSEGILEYLLQSLEFQSHPTVMLFALIALEKFAQTSENKVTVSQTCISDQLVLLEKWMDNPDYLKRQ
          .GLLS.GILEYLLQSLEFQSHPTVMLF.L.ALEKFAQTSENKVTVSQTCISDQLVLLEK.MDN.DYL..Q
Retrocopy VGLLSQGILEYLLQSLEFQSHPTVMLFVLTALEKFAQTSENKVTVSQTCISDQLVLLEKEMDNLDYLTHQ

Parental  VGFCAQWSLDNLF-LKEGRQFTYEKVDLTHINAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVD
          VGFC.QWSL.NLF.LK.GRQFT...V.LTHINAMLNSN..SEYL.IS.HGL...CDASSFESV.CT.CVD
Retrocopy VGFCTQWSLGNLF<LKYGRQFTFKEVGLTHINAMLNSNNISEYLQISLHGLNV*CDASSFESVWCTYCVD

Parental  SGVWYYEVTVVTSGVMQIGWATKDSKF
          .GV.YYEVT..TSGV..I.WATKD...
Retrocopy FGV*YYEVTIITSGVI*IRWATKDGNY

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	0.00 RPM	24.71 RPM
SRP009831_brain	0.14 RPM	9.42 RPM
SRP009831_dewlap	0.00 RPM	37.42 RPM
SRP009831_embryo	0.03 RPM	23.62 RPM
SRP009831_heart	0.00 RPM	13.23 RPM
SRP009831_liver	0.00 RPM	16.77 RPM
SRP009831_lung	0.00 RPM	22.62 RPM
SRP009831_ovary	0.00 RPM	49.30 RPM
SRP009831_skeletal_muscle	0.00 RPM	7.65 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_84 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_84 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006680	1 retrocopy	retro_acar_84 ,
Callithrix jacchus	ENSCJAG00000012138	1 retrocopy	retro_cjac_2931,