RetrogeneDB ID: retro_acar_131

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:105884692..105885094(-)
• Located in intron of: ENSACAG00000011567

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFT2D2
• Ensembl ID: ENSACAG00000010720
• Aliases: None
• Description: None

Sequence

>retro_acar_131
ATGGACAAGCTGAAGTGGGTATTGCGCGGGCAAGACGCGGAGGAGTCAGGCACCTTGCCCAAGGTGGTGGATGCATCTTC
CTTAAGCTGGAGCACAAGACCGAAAGGTTTCATAGCTTGTTCCGCTATTTGAGTTCTTTGTTCTATTTTGAATACTGGCC
TGCTATGTATTCTCAGAAAAGGACTAATCTTGTTTGCAGTATTTTATACCTTTGGAAATATCCGATCCATTAGAAGTACA
ATGTTCCTTATGGGACCTATGAGGCAACTGAAAAGAATGTTTGAAATGACTCGTTTGATAGCTACTATTGTTATGCTCCT
CTGTCCTATATTAGCACTATATGAAGCTTTCTGGTGGCATAATAAAGGACTTGCACTAATCTTCTGTGTTTTACAGTTTT
TT

Alignment

ORF - retro_acar_131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 83.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKLKRVLSGQDAEEPSPLAEVVDASSLSWSTRLKGFIACFAIGVLCSILGTCLLWVPRKGLILFAVFYT
          MDKLK.VL.GQDAEE...L..VVDASSLSWSTR.KGFIAC.AI.VLCSIL.T.LL...RKGLILFAVFYT
Retrocopy MDKLKWVLRGQDAEESGTLPKVVDASSLSWSTRPKGFIACSAI*VLCSILNTGLLCILRKGLILFAVFYT

Parental  FGNISSIGSTMFLMGPMRQLKRMFEMTRLIATIVMLLCLILTLCAAFWWHNKGLALIFCVLQFF
          FGNI.SI.STMFLMGPMRQLKRMFEMTRLIATIVMLLC.IL.L..AFWWHNKGLALIFCVLQFF
Retrocopy FGNIRSIRSTMFLMGPMRQLKRMFEMTRLIATIVMLLCPILALYEAFWWHNKGLALIFCVLQFF

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	12.11 RPM
SRP009831_brain	0.57 RPM	7.72 RPM
SRP009831_dewlap	0.00 RPM	24.47 RPM
SRP009831_embryo	0.15 RPM	14.70 RPM
SRP009831_heart	0.05 RPM	9.60 RPM
SRP009831_liver	0.04 RPM	15.46 RPM
SRP009831_lung	0.20 RPM	19.14 RPM
SRP009831_ovary	0.00 RPM	28.57 RPM
SRP009831_skeletal_muscle	0.00 RPM	2.04 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_131 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_131 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010720	1 retrocopy	retro_acar_131 ,
Callithrix jacchus	ENSCJAG00000016838	1 retrocopy	retro_cjac_2771,
Monodelphis domestica	ENSMODG00000002896	1 retrocopy	retro_mdom_607,
Mustela putorius furo	ENSMPUG00000000531	1 retrocopy	retro_mputfur_1560,
Nomascus leucogenys	ENSNLEG00000014912	1 retrocopy	retro_nleu_2370,
Rattus norvegicus	ENSRNOG00000003038	1 retrocopy	retro_rnor_1135,
Sarcophilus harrisii	ENSSHAG00000018938	1 retrocopy	retro_shar_212,
Ictidomys tridecemlineatus	ENSSTOG00000022560	1 retrocopy	retro_itri_133,