RetrogeneDB ID: retro_acar_76

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 2:9671696..9672716(+)
• Located in intron of: ENSACAG00000009088

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLT1D1
• Ensembl ID: ENSACAG00000025870
• Aliases: None
• Description: glycosyltransferase 1 domain containing 1 [Source:HGNC Symbol;Acc:26483]

Sequence

>retro_acar_76
ATGCGTGTGTTGCTCCTGGCCAGTTTGCGAGCCCGGACCGGGAATGGCACCACAGCCCAGAGGATCCAGGATCATCTGGA
AGCTGCCGGCCATGTGTGTTTCCTCAAGGACACGTTTAGCTGTGAGTCCTCTTTGGTCGTCTCAAAGCTCATCTCCTCGG
AGAACTTTGATGCAGCTCTGGCCATTCACCTTTATAAAGCAGGCAGGCTGCTGCAAGGCAGCAGAATTCCTTTTGGTGTC
ATCTTTGGAGGTACGGACATCAATGAAGATGCCAAATGTGAAGAGAAGGTCCGGGTTATGGAGGCAGTGCTGAACGAAGC
CAGGTTTGCTGTGTCTTTCACTGAGGCAATGAGAGAAAGAGCCATATCAAACTGGCCTCACGCCAGAAACAAAATATATG
TCCAGCCTCAAGGAATCGTGACTACCCCCAACATTTCTTTTAACTGGGAGAAATGTCTGCAGAGTGCAGGGATTCCCCAC
AACGGCAACAGTTTGTGTTATTTCCTCCTAATATGTGGTCTGAGAAGAGTCAAGGATCCACTCTATCTAGCAGATGCGTT
TGCAGAATGGCACAGAGAGGACCCCAGCGTACAGCTGATTATCATTGGACCTGCAGTTGATCCAGTGTTTGCAGAGGAAG
TGAAGGAGAAAGTACAAAGGGCGGATGGGGTACATTTGCTGAAGGAGATCCCCCAGGAAGACCTTCATGCTGCTGTGAAG
AAATGCTTTGCTGTTGTGAACAGTTCCATTTCAGAGGGGATGTCAGCCGCACTCTTAGAGGCCATGGATTTAAATGTTCT
AGTACTGGCAAGGAACATCCCAGGAAATGCTGCGATAATCACACACCAAGAAACCGGGCTGTTATATTCAAACCCTGAGG
AATTTGTCCAACTGTCCAAAAGCCTGATCGGTGACCCTTGTCTTCAGAGAAAGATCGTAGCAAGGGCAACGGAGTATGTC
ACAAAGCACCACTCCTGGGAACATGAAAGGAATGCTTATCAAAACTTTGTGCTGAGCCTC

Alignment

ORF - retro_acar_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRVLLLASLRARTGNGTTAQRIQDHLEAAGHVCFLKDSFSCESSLVVSKLISSENFDAALAIHLYKAGRL
          MRVLLLASLRARTGNGTTAQRIQDHLEAAGHVCFLKD.FSCESSLVVSKLISSENFDAALAIHLYKAGRL
Retrocopy MRVLLLASLRARTGNGTTAQRIQDHLEAAGHVCFLKDTFSCESSLVVSKLISSENFDAALAIHLYKAGRL

Parental  LQGSRIPFGVIFGGTDINEDTKCEEKVRVMEAVLNEARFVVSFTEAMRERAISNWPHARNKIYVQPQGIV
          LQGSRIPFGVIFGGTDINED.KCEEKVRVMEAVLNEARF.VSFTEAMRERAISNWPHARNKIYVQPQGIV
Retrocopy LQGSRIPFGVIFGGTDINEDAKCEEKVRVMEAVLNEARFAVSFTEAMRERAISNWPHARNKIYVQPQGIV

Parental  TTPNVSFNWEKCLQSAGIPHDGNSLCYFLLICGLRRVKDPLYLADAFAEWHREDPSVQLIIIGPAVDPVF
          TTPN.SFNWEKCLQSAGIPH.GNSLCYFLLICGLRRVKDPLYLADAFAEWHREDPSVQLIIIGPAVDPVF
Retrocopy TTPNISFNWEKCLQSAGIPHNGNSLCYFLLICGLRRVKDPLYLADAFAEWHREDPSVQLIIIGPAVDPVF

Parental  AEEVKEKVQRADGVHLLKEIPQEDLHAAVKKCFAVVNSSISEGMSAALLEAMDLNVPVLARNIPGNAAII
          AEEVKEKVQRADGVHLLKEIPQEDLHAAVKKCFAVVNSSISEGMSAALLEAMDLNV.VLARNIPGNAAII
Retrocopy AEEVKEKVQRADGVHLLKEIPQEDLHAAVKKCFAVVNSSISEGMSAALLEAMDLNVLVLARNIPGNAAII

Parental  THQETGLLYSNPEEFVQLSKSLISDPCLQRKIVARAKEYVTKHHSWEHERNAYQNFVLSL
          THQETGLLYSNPEEFVQLSKSLI.DPCLQRKIVARA.EYVTKHHSWEHERNAYQNFVLSL
Retrocopy THQETGLLYSNPEEFVQLSKSLIGDPCLQRKIVARATEYVTKHHSWEHERNAYQNFVLSL

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	0.03 RPM	3.32 RPM
SRP009831_brain	0.00 RPM	5.73 RPM
SRP009831_dewlap	0.08 RPM	30.29 RPM
SRP009831_embryo	0.06 RPM	7.38 RPM
SRP009831_heart	0.00 RPM	2.49 RPM
SRP009831_liver	0.00 RPM	4.54 RPM
SRP009831_lung	0.50 RPM	3.22 RPM
SRP009831_ovary	0.00 RPM	30.85 RPM
SRP009831_skeletal_muscle	0.00 RPM	0.80 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_76 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_76 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000025870	1 retrocopy	retro_acar_76 ,
Dasypus novemcinctus	ENSDNOG00000017272	2 retrocopies	retro_dnov_1218, retro_dnov_2540,