RetrogeneDB ID: retro_acar_123

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:106351316..106351760(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000005040
• Aliases: None
• Description: None

Sequence

>retro_acar_123
ATGCAGCTCAAGGTGAAGAGGCTGCTAGGACAGCAGTGCTGCCTCCAGGTATCCGGTCACGAGAGCATCTCTCTGTTGAA
AAGCCTGGTTTCAGAAGAACTGAAGGTCCCTGAGGATCAGACCACTTTGTTGTTTCAGGGCAAAGTGCTAGATGAGGACC
ACAGATTGTCAGATTATTCTATTGGCCCAGAATCCGTCCTCTATCTTGCCATTAAAAAACCTCAGCTAACGCCTCTGAAT
GAGCCCTCAAAACCCACCTTTGCCCAGGCCCATTCTGTGTGGTACCAGCTCTCCCAAGTCCTGGAGAACCACTTCAGAAC
CTCTGATGCCATAAAAGTTCTTGAAAGAGTCGTGAATGACTACTACAAAAGCCTTGGCTTATTGAGTTTGAAAAACATTG
AAGAGTTAGCCAGGGATATTCTGAATCCCAAGGAAACTGAGGCT

Alignment

ORF - retro_acar_123 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.02 %
• Parental protein coverage: 95.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLTVKALQGRECSLQVSPEERISSLKRLVSEKLNVPVSQQRLLFKGKALADEHRLSDYSIGPESKLNLV
          M.L.VK.L.G..C.LQVS..E.IS.LK.LVSE.L.VP..Q..LLF.GK.L...HRLSDYSIGPES.L.L.
Retrocopy MQLKVKRLLGQQCCLQVSGHESISLLKSLVSEELKVPEDQTTLLFQGKVLDEDHRLSDYSIGPESVLYLA

Parental  IKPPEKASPEESSRRAGFPQNPAIWHAVAQVLGRHFSGADAEKVLEQLQKDYERSLRLLSLDDIERLATR
          IK.P......E.S....F.Q....W....QVL..HF...DA.KVLE....DY..SL.LLSL..IE.LA..
Retrocopy IKKPQLTPLNEPSKPT-FAQAHSVWYQLSQVLENHFRTSDAIKVLERVVNDYYKSLGLLSLKNIEELARD

Parental  LLHPEVAEA
          .L.P...EA
Retrocopy ILNPKETEA

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	0.13 RPM	79.66 RPM
SRP009831_brain	0.14 RPM	88.95 RPM
SRP009831_dewlap	0.08 RPM	101.67 RPM
SRP009831_embryo	0.06 RPM	131.80 RPM
SRP009831_heart	0.26 RPM	58.06 RPM
SRP009831_liver	0.00 RPM	52.44 RPM
SRP009831_lung	0.15 RPM	56.62 RPM
SRP009831_ovary	0.08 RPM	102.16 RPM
SRP009831_skeletal_muscle	0.04 RPM	42.83 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_123 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_123 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005040	1 retrocopy	retro_acar_123 ,
Bos taurus	ENSBTAG00000014331	1 retrocopy	retro_btau_195,
Callithrix jacchus	ENSCJAG00000016805	1 retrocopy	retro_cjac_3272,
Ochotona princeps	ENSOPRG00000012645	1 retrocopy	retro_opri_714,
Rattus norvegicus	ENSRNOG00000037250	1 retrocopy	retro_rnor_2789,