RetrogeneDB ID: retro_acar_181

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343341.1:625974..626807(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000004255
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSACAG00000016752
• Aliases: None
• Description: ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:G1KT22]

Sequence

>retro_acar_181
ATGTTGAGCTTCGCTGGTCACCGCTGTGCCACCTCGGCTGCCTCCCTCCTACGTGGGAGTGGGACGAGGCCACTCCAGGA
TCTGCTCCAGCTTTACAGCGGGGCCATCGCCTCTGCCACCAAGGCCTGCCGAAACTATGCTGCACAAACAGCACCTGCAG
CTAAAGCTGGAGTGGCTACAGGGTGCATTGTTGCCGTCATTGGTGCTGTGGTGGATGTCCAGTTTGATGAGGCCCTGCCA
CCCATCCTCAATGCTCTGGAAGTGCAAGGCTGAGACACACAGCTGGTCCTGGAGGTAGCACAGCACTTAGGTGAGAATAC
TGTTCGTACCATTGCTATGGATGGTACTGAAGGCTTGGTGAGAGGCCAAAGGTTTTGGATTTAGGTGCCCCCATTAAAAT
CCCTGTAGGACCCGAGACCCTGGGCAGAATCATAAACGTGATTGGAGAGCCAATTGATGAGAGAGGCCCCATAACAACAA
AACAGTTTGCTGCTATTCATGCAGAAGCTCCAGCCTTTGTTGAGATGAGTGCTCGAACAGGGAAATCCCTGTCACCGGCA
TTAAAGTTGTGGATCTCCTTTGCACCTTATGCCAAAGGTGGTAAAATTGGCCTGTTTGGTGGTGCTGGTGTAGGCAAGAC
AGTATTGATCATGGAACTAATCAACAATGTTGCCAAAGCACATGGTGGCTACTCTGTGTTTGCTGGTGTTGGGAAGAGAA
CCCGTGAAGGAAATGACTTGTACCATGAAATGATTGAATCTGGAGTCATCAACCTGAAGGACGCTACATCCAAGGTCGTT
CTTGTTCATGGACAGATGAATGAGCCACCAGGA

Alignment

ORF - retro_acar_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.17 %
• Parental protein coverage: 52.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLSFAGRRCVASAASLLRGSGTRPLQDLLQLRSGAVASATEARRNYAAQTAPAAKAGVATGRIVAVIGAV
          MLSFAG.RC..SAASLLRGSGTRPLQDLLQL.SGA.ASAT.A.RNYAAQTAPAAKAGVATG.IVAVIGAV
Retrocopy MLSFAGHRCATSAASLLRGSGTRPLQDLLQLYSGAIASATKACRNYAAQTAPAAKAGVATGCIVAVIGAV

Parental  VDVQFEEALPPILNALEVQGRDTRLVLEVAQHLGENTVRTIAMDGTEGLVRGQR-VLDLGAPIRIPVGPE
          VDVQF.EALPPILNALEVQG.DT.LVLEVAQHLGENTVRTIAMDGTEGLVRGQR.VLDLGAPI.IPVGPE
Retrocopy VDVQFDEALPPILNALEVQG*DTQLVLEVAQHLGENTVRTIAMDGTEGLVRGQR<VLDLGAPIKIPVGPE

Parental  TLGRIMNVIGEPIDERGPITTKQFAAIHAEAPAFVEMS-VEQ-EILVTGIKVVDLL-APYAKGGKIGLFG
          TLGRI.NVIGEPIDERGPITTKQFAAIHAEAPAFVEMS..EQ.EI.VTGIKVVDLL.APYAKGGKIGLFG
Retrocopy TLGRIINVIGEPIDERGPITTKQFAAIHAEAPAFVEMS>LEQ>EIPVTGIKVVDLL>APYAKGGKIGLFG

Parental  GAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYHEMIESGVINLKDATSKVALVYGQMNEPP
          GAGVGKTVLIMELINNVAKAHGGYSVFAGVG.RTREGNDLYHEMIESGVINLKDATSKV.LV.GQMNEPP
Retrocopy GAGVGKTVLIMELINNVAKAHGGYSVFAGVGKRTREGNDLYHEMIESGVINLKDATSKVVLVHGQMNEPP

Parental  G
          G
Retrocopy G

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	0.10 RPM	227.69 RPM
SRP009831_brain	0.05 RPM	361.06 RPM
SRP009831_dewlap	0.00 RPM	241.22 RPM
SRP009831_embryo	0.18 RPM	673.03 RPM
SRP009831_heart	0.26 RPM	1817.54 RPM
SRP009831_liver	0.00 RPM	275.27 RPM
SRP009831_lung	0.00 RPM	139.03 RPM
SRP009831_ovary	0.04 RPM	245.32 RPM
SRP009831_skeletal_muscle	0.04 RPM	522.83 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_181 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_181 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181 ,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Callithrix jacchus	ENSCJAG00000033571	2 retrocopies	retro_cjac_1488, retro_cjac_928,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Homo sapiens	ENSG00000110955	1 retrocopy	retro_hsap_2128,
Gorilla gorilla	ENSGGOG00000011596	1 retrocopy	retro_ggor_1648,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Microcebus murinus	ENSMICG00000001084	1 retrocopy	retro_mmur_495,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Pongo abelii	ENSPPYG00000004668	2 retrocopies	retro_pabe_1921, retro_pabe_2032,
Pan troglodytes	ENSPTRG00000005107	1 retrocopy	retro_ptro_1557,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,