RetrogeneDB ID: retro_acar_162

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: GL343219.1:804036..804738(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIN
• Ensembl ID: ENSACAG00000004280
• Aliases: None
• Description: None

Sequence

>retro_acar_162
GAAAAAAAAAGAAGAAAAACACAGGGCCTTGACTATAAAGAGAAAACACCCTAGTTCAATGAGGAACAAGTGAGGAGACG
CTTTGAGGGGGAAGAACAGGAGGAGCTGGTCTTCACAGAACTAAACAGAGAAAATGAGGAAGAAAAAGTTGTATTAAGTT
TGAACAAAAGGGCAAGGAAATCAGCAGTTGCATATCCAAGGGGCCTATTTGCTTGGATCCAGTGCTCTGAAGGCAGAAGG
AACTGGACCCACGGTGATGCGCAAAGAGCCTCCTTTCAGCCCAGGGCAGACCAAAAGGAAAAAAAAAATCAGCCCTTGAC
AAAATCACACAGTTTGAAGAAGAAAAAATCGGCCAGAACAGACTATTGGTTACAGCCTGACATTGTGGTCAAAATCACTA
CCAAGAAACTTGGCAAGAAATAGTACAAAAGGAAGGCGGTGGTAAAGGAGACAATTGACAAACATACTGCAGTTGTTAAA
ATGATCGATTCCGCAGACAAGCTGAAGCTTGATCAGATTCATCTAGAGACAGTGATTCCAGCACCTGGCAAAAGGGTGTG
TGTTTTGAATGGTGGCTACAGAGGACAAGCGAGTTTGCAGGGCATCAATGAGAAATCCTTTTTAGCCACCATAATTGAAT
CCAGGCCTCTGAAAGGACATCAAGTTGAGGATGTCTCATGTGAAAACATTTTGAAGTTGGCT

Alignment

ORF - retro_acar_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.78 %
• Parental protein coverage: 65.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EQEKKKKQDLDDEEKTARFIEEQVKRGLEGKEQQEEPVFTELSRESEEEKVVFNLNKGASTSTAAHPK-A
          E....K.Q.LD..EKT..F.EEQV.R..EG.E.QEE.VFTEL.RE.EEEKVV..LNK.A..S..A.P..A
Retrocopy EKKRRKTQGLDYKEKTP*FNEEQVRRRFEG-EEQEELVFTELNRENEEEKVVLSLNKRARKSAVAYPR>A

Parental  NVLGSSALKAAGTVPTVKRKEPPSNPGQTK-KKKSALDEIMQFEEEKKKSTRTDYWLQPDIVVKIITKKL
          ..LGSSALKA.GT.PTV.RKEPP..PGQTK.K.K............KKKS.RTDYWLQPDIVVKI.TKKL
Retrocopy YLLGSSALKAEGTGPTVMRKEPPFSPGQTK<KEKKNQPLTKSHSLKKKKSARTDYWLQPDIVVKITTKKL

Parental  GEKYHKKKAVIKEVIDKYTAVVKTIDSGDRLKLDQTHLETVIPAPGKRVRVLNGGYRGQEATLQGINEKM
          G.K..K.KAV.KE.IDK.TAVVK.IDS.D.LKLDQ.HLETVIPAPGKRV.VLNGGYRGQ.A.LQGINEK.
Retrocopy GKK*YKRKAVVKETIDKHTAVVKMIDSADKLKLDQIHLETVIPAPGKRVCVLNGGYRGQ-ASLQGINEKS

Parental  FSATIIIESGPLKGRQVEGIPYEDISKLA
          F.AT.IIES.PLKG.QVE....E.I.KLA
Retrocopy FLAT-IIESRPLKGHQVEDVSCENILKLA

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	59.54 RPM
SRP009831_brain	0.14 RPM	36.36 RPM
SRP009831_dewlap	0.00 RPM	86.86 RPM
SRP009831_embryo	0.00 RPM	35.42 RPM
SRP009831_heart	0.10 RPM	24.90 RPM
SRP009831_liver	0.04 RPM	208.60 RPM
SRP009831_lung	0.30 RPM	35.41 RPM
SRP009831_ovary	0.00 RPM	74.28 RPM
SRP009831_skeletal_muscle	0.00 RPM	5.61 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_162 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_162 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162 ,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281, retro_cpor_818, retro_cpor_987, retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344, retro_dord_657,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9,