RetrogeneDB ID: retro_acar_146

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 6:63688856..63689942(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KATNB1
• Ensembl ID: ENSACAG00000000837
• Aliases: None
• Description: None

Sequence

>retro_acar_146
ATCATGAATATACAGAAAGGAACAACGCTGGTGGAGAGCATGAAGATCAACACCAAAGAAGAGCTGATCGTTGCCGGGTC
TCAGTCCGGCTCTATTCGCATCTGGGACCTGGAGGCTGCCAAAATTCTCCGCACCTTAATGGGCCACAAAGCCAACATCT
GAAGCCTGGACTTCCATCCGTTCGGGGGTTTCGTGGCCTCGGGATCCATGGACACCAACATTAAGCTTTGGGATGTGAGA
AGGAAAGGCTGCATCTTCAGGTACAAAGGCCACTCGCAGGCCGTCCGCTGCCTCCGCTTCAGCCCAGATGGGAAATGGCT
GGCGTCTTCCTCGGACAATCACACGGTGAAGCTCTGGGACCTGGCTGCTGGGAAGATCATGTTTGAGTTCGCGGGACACA
TGGGGCCAGTGAACATGGTGGAATTCCATCCCAACGAATACCTTTTGGCCTCGGGGAGCTCCGACAGAATGATCAGGTTC
TGGGACTTGGAGAAGTTCCAGGTGGTGAGCTGCATCGAGGAAGAGGCCACACCTGCCAGGTGCGTCCTCTTCAACCCAGA
CGGCTGCTGCCTCTTTGCCGGCTGCCAGGACACCCTGCGGGTTTACGGCTGGGAACCGGAGCGCTGCTTTGACGTAGTGC
CCATCAGCTGGGGCAAAGTGGCCGACCTCTCCATCTGCAACAACCAGCTGATCGGCGTCTCCTTCTCGCAAAGCGTGGTC
TCCTCCTTCGTGGTGGACCTCAACCGCGTCACCAGATCTGGCTCCGGCCTCCAGGGCCTGATCCGGGATGACCGACCCCT
CGCACAGCAGCTCCCAGCAACCGGATCCTCCCTGCGGCACATCTACGAACGGCCCTCCGCTGCATGCAGCAAACCTCAGC
GAGTCAAACACAACTCGGAGAGCGAGAGGCGCAGCCCCAGCAGCGAAGACGACCGGGAAGAGAAGGAATCCACCGCTGAA
ATCCAGAATGCAGAGGATTACCAAGAGATCTTCCAGCCAAAGAATTCCATCACCCGAACTCCTCCGCACAAGAGTGAGCC
TTTTCCTGCACCTCCGGAAGATGAACCACCGCCGGTTGCCAAAGAA

Alignment

ORF - retro_acar_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IMSLTGHTTPVESVKINTNEELIVAGSQSGSIRIWDLEAAKILRTLMGHKANICSLDFHPFGGFVASGSM
          IM.....TT.VES.KINT.EELIVAGSQSGSIRIWDLEAAKILRTLMGHKANI.SLDFHPFGGFVASGSM
Retrocopy IMNIQKGTTLVESMKINTKEELIVAGSQSGSIRIWDLEAAKILRTLMGHKANI*SLDFHPFGGFVASGSM

Parental  DTNIKLWDVRRKGCVFRYKGHSQAVRCLRFSPDGKWLASSSDDHTVKLWDLAAGKIMFEFAGHTGPVNMV
          DTNIKLWDVRRKGC.FRYKGHSQAVRCLRFSPDGKWLASSSD.HTVKLWDLAAGKIMFEFAGH.GPVNMV
Retrocopy DTNIKLWDVRRKGCIFRYKGHSQAVRCLRFSPDGKWLASSSDNHTVKLWDLAAGKIMFEFAGHMGPVNMV

Parental  EFHPNEYLLASGSSDRMIRFWDLEKFQVVSCIEEEATPARCVLFNPDGCCLFAGCQDALRVYGWEPERCF
          EFHPNEYLLASGSSDRMIRFWDLEKFQVVSCIEEEATPARCVLFNPDGCCLFAGCQD.LRVYGWEPERCF
Retrocopy EFHPNEYLLASGSSDRMIRFWDLEKFQVVSCIEEEATPARCVLFNPDGCCLFAGCQDTLRVYGWEPERCF

Parental  DVVPVSWSKVADLSICNNQLIGVSFSQSVVSSFVVDLNRVTRSGSGLQGLIRDDRPPAQQLPPTGSSLRR
          DVVP.SW.KVADLSICNNQLIGVSFSQSVVSSFVVDLNRVTRSGSGLQGLIRDDRP.AQQLP.TGSSLR.
Retrocopy DVVPISWGKVADLSICNNQLIGVSFSQSVVSSFVVDLNRVTRSGSGLQGLIRDDRPLAQQLPATGSSLRH

Parental  IYERPSTACSKPQRVKHNSESERRSPSSEDDREEKESTAEIQNPEDYQEIFQPKNSITRTPPHKSEPFPA
          IYERPS.ACSKPQRVKHNSESERRSPSSEDDREEKESTAEIQN.EDYQEIFQPKNSITRTPPHKSEPFPA
Retrocopy IYERPSAACSKPQRVKHNSESERRSPSSEDDREEKESTAEIQNAEDYQEIFQPKNSITRTPPHKSEPFPA

Parental  PPEDEPPPVAKE
          PPEDEPPPVAKE
Retrocopy PPEDEPPPVAKE

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	1.54 RPM	4.79 RPM
SRP009831_brain	1.56 RPM	18.27 RPM
SRP009831_dewlap	71.46 RPM	43.33 RPM
SRP009831_embryo	12.06 RPM	66.86 RPM
SRP009831_heart	0.83 RPM	25.73 RPM
SRP009831_liver	0.70 RPM	4.09 RPM
SRP009831_lung	0.50 RPM	14.41 RPM
SRP009831_ovary	80.31 RPM	70.58 RPM
SRP009831_skeletal_muscle	0.73 RPM	4.22 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_146 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_146 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000837	1 retrocopy	retro_acar_146 ,