RetrogeneDB ID: retro_acar_133

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 5:66517911..66518652(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000014253
• Aliases: None
• Description: None

Sequence

>retro_acar_133
ATGCTGGGCTCCAGGACTTTACTGCAGGGAGCCATGGTGGCAGCATGGGAGATCGCTGCCCAGGTTTCATAATCTTTTGC
TATTGGGCCCAGACAACATGATGGCACATTCTATGATTTCTGTACCTATACTGTTAAGCCAAGCAAGATGGAAGAGTTTT
TGGATCTGACTAGTTGAAACATCCACTTCTACACAGCTCATTCTCCCATGCTTGGCTACTGGACTTTGGAGTTGGGAGGA
CTGGAGAAAACATTCTATATTTGGAAGTATGAAAGCTTTGCCCAAAAAACTGCTGTCCGGACAGCGTTAGCCAAAGACCA
AGCCTGGCAAGAAAAATGTTTGTCTCAAATGTTTCCCTTGTTAGAAAGACAAGACAATGAGATTGCCTACCTAGTTCCTT
TGGTGTGAACTTGGAAGCTCTGAAAAGGATGGAGTCTATGAGTTGGTTAACTTCCACATGAAACCTGGTGGACCAGCAAT
GTGGGGACAATCCTTTAAAAAGACAATTTATGCTCATGTGAAGATGGGATACACTAAGCTGATTGGCGTCTTCCATACAG
ATATGGAAAACTTAACAGAGTTCATGTACTCTGGTGGAATGAGAGCCCAGATAGTCAGGCATCCAGAAGGCACTATGTAC
ACAAAGATCCAAGAGTAGTCGTTGCTGTTCATGAACATGTTCAGTTCTTGGAAGCTCAGCAGACCTGCCTTCTGGTGCCT
ACTGCATTCTCACCACTAAAA

Alignment

ORF - retro_acar_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLGPRTLLRGALAAARGFPGQVSSSFATGPRQHDGTFYEFRTYTVKPSKMKEFLDLTNKNIHLRTAHSPL
          MLG.RTLL.GA..AA.....QVS.SFA.GPRQHDGTFY.F.TYTVKPSKM.EFLDLT..NIH..TAHSP.
Retrocopy MLGSRTLLQGAMVAAWEIAAQVS*SFAIGPRQHDGTFYDFCTYTVKPSKMEEFLDLTS*NIHFYTAHSPM

Parental  VGYWTLELGGLNKTFHIWKYESFAQRTAVRTALANDQAWKEKYLSQMLPMLDKQENEIAYLVP-WCELGS
          .GYWTLELGGL.KTF.IWKYESFAQ.TAVRTALA.DQAW.EK.LSQM.P.L..Q.NEIAYLVP.WCELGS
Retrocopy LGYWTLELGGLEKTFYIWKYESFAQKTAVRTALAKDQAWQEKCLSQMFPLLERQDNEIAYLVP>WCELGS

Parental  SEKDGVYELVTFNMKPGGPAVWGQSFKAAINAHVKTGYTKLIGVFHTE-YGNLNRVHVLWWSESPDSRAS
          SEKDGVYELV.F.MKPGGPA.WGQSFK..I.AHVK.GYTKLIGVFHT..YG.LNRVHVLWW.ESPDS.AS
Retrocopy SEKDGVYELVNFHMKPGGPAMWGQSFKKTIYAHVKMGYTKLIGVFHTD<YGKLNRVHVLWWNESPDSQAS

Parental  GRHYAHEDPRVVAAVRESVQFLESQQNCLLVPTAFSPLK
          .RHY.H.DPRVV.AV.E.VQFLE.QQ.CLLVPTAFSPLK
Retrocopy RRHYVHKDPRVVVAVHEHVQFLEAQQTCLLVPTAFSPLK

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	16.05 RPM
SRP009831_brain	0.00 RPM	35.27 RPM
SRP009831_dewlap	0.00 RPM	25.90 RPM
SRP009831_embryo	0.00 RPM	62.48 RPM
SRP009831_heart	0.00 RPM	4.25 RPM
SRP009831_liver	0.00 RPM	164.43 RPM
SRP009831_lung	0.00 RPM	7.15 RPM
SRP009831_ovary	0.00 RPM	27.72 RPM
SRP009831_skeletal_muscle	0.00 RPM	3.72 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_133 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_133 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133 ,
Ailuropoda melanoleuca	ENSAMEG00000005118	1 retrocopy	retro_amel_552,
Canis familiaris	ENSCAFG00000023949	1 retrocopy	retro_cfam_295,
Cavia porcellus	ENSCPOG00000009373	1 retrocopy	retro_cpor_690,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482,
Equus caballus	ENSECAG00000008088	1 retrocopy	retro_ecab_978,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Myotis lucifugus	ENSMLUG00000010147	1 retrocopy	retro_mluc_924,
Mustela putorius furo	ENSMPUG00000007103	1 retrocopy	retro_mputfur_1471,
Oryctolagus cuniculus	ENSOCUG00000007880	1 retrocopy	retro_ocun_1385,
Tursiops truncatus	ENSTTRG00000012307	1 retrocopy	retro_ttru_1702,