RetrogeneDB ID: retro_acar_138

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 5:5372032..5372316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB2
• Ensembl ID: ENSACAG00000011176
• Aliases: None
• Description: None

Sequence

>retro_acar_138
CTTTGCCAGGTGAATGCCAGAGTCTGTCACTCAAGAAGTAGTACAGGCACAACCTTGGGAGTCTGGCATGCCAGTGGAGG
TATAGACATGGGACCTTGCTACTGCCAATTCTTAGAGCCGACACAGTCACGACAGATAAAAGCTTAGATGCTCATTAGCC
TGATGTTATTCTGAGTTCTGTGGCACTTCTGGCAAGATCGAATGCTGTGCTGGGCCATTTTCCTTCTCCAATTCTTTCTA
AGTGAACAGATGAAGAGCTAGGAGACCCTCTTGGGGAGGAAGAC

Alignment

ORF - retro_acar_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.04 %
• Parental protein coverage: 92.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCRAATRVLRAGRGLGVAGGVRRASGGVHIEPRYRQFPELTRSQQIKAEVLSSLMWFWILWKFWHD-PDA
          LC....RV.......G...GV..ASGG....P.Y.QF.E.T.S.QIKA..L.SLM.F..LW.FW.D...A
Retrocopy LCQVNARVCHSRSSTGTTLGVWHASGGIDMGPCYCQFLEPTQSRQIKA*MLISLMLF*VLWHFWQD<SNA

Parental  VLGHFPYPDPSQWTDEELGIPPDDEE
          VLGHFP.P..S..TDEELG.P...E.
Retrocopy VLGHFPSPILSK*TDEELGDPLGEED

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	91.47 RPM
SRP009831_brain	0.00 RPM	65.28 RPM
SRP009831_dewlap	0.00 RPM	87.88 RPM
SRP009831_embryo	0.00 RPM	40.28 RPM
SRP009831_heart	0.00 RPM	78.45 RPM
SRP009831_liver	0.04 RPM	131.34 RPM
SRP009831_lung	0.35 RPM	46.54 RPM
SRP009831_ovary	0.00 RPM	98.72 RPM
SRP009831_skeletal_muscle	0.00 RPM	70.80 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_138 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_138 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011176	1 retrocopy	retro_acar_138 ,
Canis familiaris	ENSCAFG00000003930	3 retrocopies	retro_cfam_1673, retro_cfam_2184, retro_cfam_958,
Equus caballus	ENSECAG00000000877	1 retrocopy	retro_ecab_587,
Mustela putorius furo	ENSMPUG00000003423	3 retrocopies	retro_mputfur_132, retro_mputfur_1443, retro_mputfur_207,
Mus musculus	ENSMUSG00000002416	1 retrocopy	retro_mmus_1881,
Otolemur garnettii	ENSOGAG00000009644	1 retrocopy	retro_ogar_1405,
Ochotona princeps	ENSOPRG00000013184	2 retrocopies	retro_opri_1201, retro_opri_143,
Rattus norvegicus	ENSRNOG00000026616	2 retrocopies	retro_rnor_1153, retro_rnor_2449,
Sarcophilus harrisii	ENSSHAG00000015924	1 retrocopy	retro_shar_639,
Sus scrofa	ENSSSCG00000016495	1 retrocopy	retro_sscr_1149,
Ictidomys tridecemlineatus	ENSSTOG00000002566	1 retrocopy	retro_itri_1100,
Tursiops truncatus	ENSTTRG00000000547	2 retrocopies	retro_ttru_1567, retro_ttru_1910,