RetrogeneDB ID: retro_acar_40

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: AAWZ02037698:641..1379(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000002258
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GNAI3
• Ensembl ID: ENSACAG00000010970
• Aliases: None
• Description: None

Sequence

>retro_acar_40
ACCATGGGATGCCGGCAAAGCTCGGAGGAGAAAGAGGCGGCGCGGCGGTCCCGGCGGATCGACCGGCACCTGCGCTCGGA
GAGCCAGCGCCAGCGCCGGGAGATCAAGCTGCTCCTGCTGGGGACCAGCAACTCCGGGAAGAGCACCATCGTTAAGCAGA
TGAAGATCATCCACAGCGGCGGGTTCAACCTGGAGGCCTGCAAGGAGTACAAGCCGCTCATCATCTACAACGCCATCGAC
TCGCTCACCCGCATCATCCGGGCGCTGGCCACCCTCAAGATCGAGTTCCACAACCCGGACCGGGCCTACGACGCGGTGCA
GCTCTTTGCGCTGACGGGCCCCGCGGAGAGCAAGGGGGAGATCACGCCCGAGCTGCTGGGGGTCATGAGGCGGCTGTGGG
GCGACCCCGGGGTGCAGGAGTGCTTCTGCCGCTCCAGCGAGTACCACCTGGAGGACAACGCCGCCTACTACCTGAACGAC
CTGGAGCGCATCGCGGCCGCGGACTACATCCCCACGGTGGAGGACATCCTGCGCTCCCGGGACATGACCACGGGCATCGT
GGAGAACAAGTTCACCTTCAAGGAGCTGACCTTCAAGATGGTGGACGTGGGCGGGCAGCGCTCCGAGCGCAAGAAGTGGA
TCCACTGCTTCGAGGGCGTCACCGCCATCATCTTCTGCGTCGAGCTGAGCGGATACGACCTCAAGCTGTACGAGGACAAC
CAGACGGTAAGGCCCGCC

Alignment

ORF - retro_acar_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.37 %
• Parental protein coverage: 68.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCTLSAEDKAAVERSRMIDRNLREDGEKAAKEVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECKQYK
          MGC..S.E.K.A..RSR.IDR.LR........E.KLLLLG...SGKSTIVKQMKIIH..G...E.CK.YK
Retrocopy MGCRQSSEEKEAARRSRRIDRHLRSESQRQRREIKLLLLGTSNSGKSTIVKQMKIIHSGGFNLEACKEYK

Parental  VVVYSNTIQSIIAIIRAMGRLKIDFGEVARADDARQLFVLAGSAE-EGVMTPELAGVIKRLWRDPGVQAC
          .....N.I.S...IIRA...LKI.F....RA.DA.QLF.L.G.AE..G..TPEL.GV..RLW.DPGVQ.C
Retrocopy PLIIYNAIDSLTRIIRALATLKIEFHNPDRAYDAVQLFALTGPAESKGEITPELLGVMRRLWGDPGVQEC

Parental  FSRSREYQLNDSASYYLNDLERISQQNYIPTQQDVLRTRVKTTGIVETHFTFKDLYFKMFDVGGQRSERK
          F.RS.EY.L.D.A.YYLNDLERI....YIPT..D.LR.R..TTGIVE..FTFK.L.FKM.DVGGQRSERK
Retrocopy FCRSSEYHLEDNAAYYLNDLERIAAADYIPTVEDILRSRDMTTGIVENKFTFKELTFKMVDVGGQRSERK

Parental  KWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNR
          KWIHCFEGVTAIIFCV.LS.YDL.L.ED....R
Retrocopy KWIHCFEGVTAIIFCVELSGYDLKLYEDNQTVR

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	0.72 RPM	97.42 RPM
SRP009831_brain	5.49 RPM	100.17 RPM
SRP009831_dewlap	0.63 RPM	140.02 RPM
SRP009831_embryo	2.05 RPM	168.73 RPM
SRP009831_heart	1.14 RPM	37.04 RPM
SRP009831_liver	0.53 RPM	81.64 RPM
SRP009831_lung	1.71 RPM	145.68 RPM
SRP009831_ovary	1.00 RPM	114.20 RPM
SRP009831_skeletal_muscle	0.18 RPM	6.88 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_40 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_40 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010970	1 retrocopy	retro_acar_40 ,
Choloepus hoffmanni	ENSCHOG00000012718	1 retrocopy	retro_chof_359,
Ciona intestinalis	ENSCING00000005305	1 retrocopy	retro_cint_14,
Ciona savignyi	ENSCSAVG00000001800	1 retrocopy	retro_csav_19,
Otolemur garnettii	ENSOGAG00000013587	1 retrocopy	retro_ogar_993,
Tupaia belangeri	ENSTBEG00000015771	1 retrocopy	retro_tbel_2449,
Tarsius syrichta	ENSTSYG00000000556	1 retrocopy	retro_tsyr_288,