RetrogeneDB ID: retro_acar_113

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 3:194342886..194343810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANKRD29
• Ensembl ID: ENSACAG00000000289
• Aliases: None
• Description: ankyrin repeat domain 29 [Source:HGNC Symbol;Acc:27110]

Sequence

>retro_acar_113
ATGAACAGCGTGGGCTGTGGTGAGCTCAAGATATATTTCAAGAAGGCGACACCATTGACAAATGCTGCATTCTGAGATGC
TAGGCAAGGAAACTTGGTCCTCCTACAGCTGTTGTTGAACAGTGGGCATGCTGATGTGGACTGCAAAGACAGTCTTGTTC
AACAGTTCTTATGGTAGCATTGTTCTATGGCCACAAAGAATGTTTATGGGAATTGGTAATGAAAGTAGCTGATATTAATC
TTCAGAGAGAGACTGGTGTCACTGCTGTTCTTTACTGCACAACAAGGCCACAATGATATTTTGAAGTTACTCTTTGAGTA
TGAAGTCTCCACAGAGTTTAAAACCAAACATGGAGGCATTACTTTGTTAGTGGCTTGCCGATATGGACACGTAAGAGTAG
TGGAAATGTTACTAAAGCATGGCACCAACATCCACAATCAGCTTTATGATGGAGCTACTTCCCTTTTCTTGGCTGCTCAA
GAAGGATATATGGACTTAATTAAGTTATTACTGTCTTCAAGAGAAAAGGTCAATCAGCCAAGGTAGGACGGGACAGCTCT
ATTGTGGATTGTCTCTTAGATGGACCACAGTGAGATAATGTGAATAATGTTACTCCGAGGGACTGACCAAGATGTGGCAA
GAAGTGATGGCACAAACAACACTTTACTTAAAGCTGCAAACAAAGGATATAGTAGTGTTATAGAATAATTGCTTAAAGTC
TCCCCTTTATTTGGTTTACTGAAGAGCAGGACATCGGCTCTCCATGCTGCAGGTCTTAGTGGCAGAGTTAGAGCAATTGC
ACTACTCTTAGAAGCAGGAGCTGATCCATTCCTTAGAAAAAAGAAAAATGAGCTGCTTTCAGATCTCAAGAAAAATAAGT
GCATCCTGTGACTCCTGAAACTTAGAAAAAAGGACAGAAAAAGC

Alignment

ORF - retro_acar_113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSEGWAEFKMSFKKETPLANAAFWAARKGNLALLQLLLNSGRVDVDCKDSL-GSTALMVASYYGHKECV
          M.S.G..E.K..FKK.TPL.NAAF..AR.GNL.LLQLLLNSG..DVDCKDSL..ST.LMVA..YGHKEC.
Retrocopy MNSVGCGELKIYFKKATPLTNAAF*DARQGNLVLLQLLLNSGHADVDCKDSL<CSTVLMVALFYGHKECL

Parental  RELVLQGADINLQRETGATAL-FFAAQQGHNDIVKLLFEYGASTEFKTKDGGTALLAACQYGHMRVVETL
          .ELV...ADINLQRETG.TA..F.A.Q.GHNDI.KLLFEY..STEFKTK.GG..LL.AC.YGH.RVVE.L
Retrocopy WELVMKVADINLQRETGVTAV>FTAQQ-GHNDILKLLFEYEVSTEFKTKHGGITLLVACRYGHVRVVEML

Parental  LKHGANIHDQLYDGATALFLAAQGGYLDLIRLLLSSGAKVNQPRQDGTAPLWIASQMGHSEIVRVMLLRG
          LKHG.NIH.QLYDGAT.LFLAAQ.GY.DLI.LLLSS..KVNQPR.DGTA.LWI.S.M.HSEI...MLLRG
Retrocopy LKHGTNIHNQLYDGATSLFLAAQEGYMDLIKLLLSSREKVNQPR*DGTALLWIVS*MDHSEIM*IMLLRG

Parental  ADRDAARSDGT-TPLLKAANKGYSSVIEELLKFSPSLGLLKSGTTALHAAVLGGSVKVVALLLEAGADPF
          .D.D.ARSDGT...LLKAANKGYSSVIE.LLK.SP..GLLKS.T.ALHAA.L.G.V...ALLLEAGADPF
Retrocopy TDQDVARSDGTNNTLLKAANKGYSSVIE*LLKVSPLFGLLKSRTSALHAAGLSGRVRAIALLLEAGADPF

Parental  LRNKKNELPSDLTKNERILRLLQPREKDRKS
          LR.KKNEL.SDL.KN..IL.LL..R.KDRKS
Retrocopy LRKKKNELLSDLKKNKCIL*LLKLRKKDRKS

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	5.25 RPM
SRP009831_brain	0.00 RPM	15.01 RPM
SRP009831_dewlap	0.00 RPM	18.27 RPM
SRP009831_embryo	0.00 RPM	16.83 RPM
SRP009831_heart	0.00 RPM	5.29 RPM
SRP009831_liver	0.00 RPM	1.88 RPM
SRP009831_lung	0.00 RPM	4.18 RPM
SRP009831_ovary	0.00 RPM	20.08 RPM
SRP009831_skeletal_muscle	0.00 RPM	2.73 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_113 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_113 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000289	1 retrocopy	retro_acar_113 ,