RetrogeneDB ID: retro_acar_155

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343196.1:2006231..2006807(+)
• Located in intron of: ENSACAG00000008935

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSACAG00000011052
• Aliases: None
• Description: None

Sequence

>retro_acar_155
TATTTAAGATTGAGTGGCGTTTATTGGGGATTAACAGTAATGGATCTTATGCGACAGCTGCATCGTATGAGCAAAGAAGA
AATTCTGGAATTTATCAAATCATGTCAACATGAATGTGGGAGAATAAATGCCAGCATAGGTCATGATCCTCATCTTTTAT
ATACCCTTAGTGCTGTCCAGATTCTAACACTTTATGACAGTCTCTAGGTTGTTGATGTAAATAAGATTGTAGAATATAAG
AAGAAGCTGCAAAAGGAGGATGGATCATTTGCTGGAGATAAATTGGGAGAAGTAGATACAAGGTTTTCTTTTTGTGCAGT
TGCAACGTTAGCCCTTCTGGGCAAACTGGATGCCATTGATGTGGACAAAGCAGTAGCATTTGTATTGTCCTGTATGAACT
TTGATGGAGGGTTTGGTTGTAGACCAGGATCTGAATCTCATGCAGGACAGATCTATTGTTGCACAGGATTTCTAGCCATA
ACTGGCCAGCTGCATCAAATTAATGCTGATCTACTAGGCTGGTGGCTTTGTGAACGTCAGTTACCATCTGGAGGGCTAAA
TGGAAGGCCAGAGAAG

Alignment

ORF - retro_acar_155 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.35 %
• Parental protein coverage: 56.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLRMSGVYWGLTVMDLMGQLHRMSKEEILEFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSLQV
          YLR.SGVYWGLTVMDLM.QLHRMSKEEILEFIKSCQHECG.I.ASIGHDPHLLYTLSAVQILTLYDSL.V
Retrocopy YLRLSGVYWGLTVMDLMRQLHRMSKEEILEFIKSCQHECGRINASIGHDPHLLYTLSAVQILTLYDSL*V

Parental  VDVNKIVEYVKKLQKEDGSFAGDKWGEVDTRFSFCAVATLALLGKLDAIDVDKAVAFVLSCMNFDGGFGC
          VDVNKIVEY.KKLQKEDGSFAGDK.GEVDTRFSFCAVATLALLGKLDAIDVDKAVAFVLSCMNFDGGFGC
Retrocopy VDVNKIVEYKKKLQKEDGSFAGDKLGEVDTRFSFCAVATLALLGKLDAIDVDKAVAFVLSCMNFDGGFGC

Parental  RPGSESHAGQIYCCTGFLAITGQLHQINADLLGWWLCERQLPSGGLNGRPEK
          RPGSESHAGQIYCCTGFLAITGQLHQINADLLGWWLCERQLPSGGLNGRPEK
Retrocopy RPGSESHAGQIYCCTGFLAITGQLHQINADLLGWWLCERQLPSGGLNGRPEK

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	45.56 RPM
SRP009831_brain	0.00 RPM	69.87 RPM
SRP009831_dewlap	0.04 RPM	117.07 RPM
SRP009831_embryo	0.18 RPM	119.44 RPM
SRP009831_heart	0.00 RPM	27.03 RPM
SRP009831_liver	0.00 RPM	24.99 RPM
SRP009831_lung	0.15 RPM	20.75 RPM
SRP009831_ovary	0.04 RPM	102.00 RPM
SRP009831_skeletal_muscle	0.00 RPM	20.91 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_155 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_155 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155 ,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,