RetrogeneDB ID: retro_acar_62

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 1:259852776..259853349(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NTAN1
• Ensembl ID: ENSACAG00000003857
• Aliases: None
• Description: None

Sequence

>retro_acar_62
AGGCACACAGGTAATGGAGCTACATGCCCGATGCATTGCGATGGGTCAGATACAGAAATGGAAGAACTGTCGATGATGAA
TGCAATCAAAGTGCTTTCTTCTAACACAGAGTGTGGAAGGTTGGAGGTACACCTGACTGGAGGTTTCAATGACGATAGGC
ATTTATCCCAGCAACTTACCAACCAGCTTCTTAGAGCATTTGACAACTTGCAGAACAGCATCCATTTAGTGACTTTCTGC
GTGACAGATTTAAATGACAGGCAGGAAAAAGGCAACAACTTTCTGTTTATATATGGAATTACTGTAAATGTTAAAACCGG
AGAGGTTTTCCACACCACATTTCCAGACAGGGGATCTGTTGAGGATTTGCGTTCCGCCAGTATATTAACAGGAGCCAAGA
TGGTTAACATTTATGATTCAAGAAAGGAAGAGCTTAGCATTGAGCCTTATTTCTGGATGCCTTTCCCCCATGTCGATATC
TGGCTACAACAGGACAACTAACACATATTGCAGATTCTCTCCATTTCGCCAGTAGCTGAACCCCCTCATTTTGTTTCCCA
TATTCGGGCAACC

Alignment

ORF - retro_acar_62 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.25 %
• Parental protein coverage: 61.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RHTGSGATCLTHCDGSDTEMEVLLMMNAIKMLSSNTECGRLEVHLVGGFNDDRHLSQQLTNQLLKAFKQR
          RHTG.GATC..HCDGSDTEME.L.MMNAIK.LSSNTECGRLEVHL.GGFNDDRHLSQQLTNQLL.AF...
Retrocopy RHTGNGATCPMHCDGSDTEMEELSMMNAIKVLSSNTECGRLEVHLTGGFNDDRHLSQQLTNQLLRAFDNL

Parental  LDAINLIIIIIITDLNDRQEKGNHFPFLYGIAVNVKTGEVFHATFPDRGPAEDLRSASILTGAKMVNIYD
          ...I.L......TDLNDRQEKGN.F.F.YGI.VNVKTGEVFH.TFPDRG..EDLRSASILTGAKMVNIYD
Retrocopy QNSIHLVTFCV-TDLNDRQEKGNNFLFIYGITVNVKTGEVFHTTFPDRGSVEDLRSASILTGAKMVNIYD

Parental  SRKEELRIGPYFWMPFPHVDFWLQQDDEHILQNLSTSPLAEPPHFVSHIRAT
          SRKEEL.I.PYFWMPFPHVD.WLQQD..HILQ.LS.SP.AEPPHFVSHIRAT
Retrocopy SRKEELSIEPYFWMPFPHVDIWLQQDN*HILQILSISPVAEPPHFVSHIRAT

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	11.42 RPM
SRP009831_brain	0.09 RPM	14.39 RPM
SRP009831_dewlap	0.08 RPM	32.82 RPM
SRP009831_embryo	0.03 RPM	33.58 RPM
SRP009831_heart	0.10 RPM	20.18 RPM
SRP009831_liver	0.00 RPM	14.44 RPM
SRP009831_lung	0.00 RPM	22.21 RPM
SRP009831_ovary	0.35 RPM	33.74 RPM
SRP009831_skeletal_muscle	0.04 RPM	14.39 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_62 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_62 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003857	1 retrocopy	retro_acar_62 ,
Choloepus hoffmanni	ENSCHOG00000011818	3 retrocopies	retro_chof_1148, retro_chof_1591, retro_chof_2046,
Dasypus novemcinctus	ENSDNOG00000016017	5 retrocopies	retro_dnov_1068, retro_dnov_1159, retro_dnov_129, retro_dnov_874, retro_dnov_97,
Echinops telfairi	ENSETEG00000014054	1 retrocopy	retro_etel_1914,
Microcebus murinus	ENSMICG00000014995	2 retrocopies	retro_mmur_1479, retro_mmur_959,
Myotis lucifugus	ENSMLUG00000003455	1 retrocopy	retro_mluc_1398,
Mustela putorius furo	ENSMPUG00000014327	1 retrocopy	retro_mputfur_762,
Otolemur garnettii	ENSOGAG00000002538	2 retrocopies	retro_ogar_706, retro_ogar_78,
Pteropus vampyrus	ENSPVAG00000002982	1 retrocopy	retro_pvam_626,
Tupaia belangeri	ENSTBEG00000014096	2 retrocopies	retro_tbel_3921, retro_tbel_905,