RetrogeneDB ID: retro_acar_34

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: AAWZ02038596:2228..3995(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000026225
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSACAG00000023302
• Aliases: None
• Description: None

Sequence

>retro_acar_34
ATGGAGGACAAAGCTTCTAAAGCCCTGCAGTGTGGAAAGTGTTTCACACGGAGGGCTCATCTGCAGCAACATGAAAAGAT
TCATACTGGAGATGAACACTATGAATGCATGGAGTGTGGAAACAACTTCACTCATAATTCAAATCTGCATCAAAATAGTC
ACACTGGGGAGAAACCCTATACATGCCTGGAGTGTGGACAGAGCTACACTCGGATTGCAAATCTACATTCACATGAAAGG
ACTCACACTGGAGAGAAACCCTATACATGCCTGGAGTGTGGAAAAAGCTTTGCTCAGAGTGTACATCTACGTTCACATCA
GAGGACCCACACTGGAAAGAAACCCTATAAATGCTTAGAGTGTGGACAGAACTTCACTAATAATGGAAATCTACGTAGAC
ATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCTTGGAGTGTGGACAGAGTTTCACTGATAGTTCAAGTCTACGT
TCACATCAGAGGACTCACACTGGGGAGAAACCCTATAAATGCTTGGAGTGTGGACAGAGTTTCACTGATAGTTCAAGTCT
ACGTTCACATCAGAGGACTCACACTGGGGAGAAACCCTATAAATGCTTGGAGTGTGGACTGAGTTACACTCGGAGTGCAA
GTCTATATTCACATTTAAGGACTCACACTGGGGAGAAACCTTATACATGCCTGGAGTGTGGACAGAGCTTCATTCTCAGT
TCAAGTCTATATTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTCACTCA
TAGTTCAACTCTACGTAAACATCAAAGAACTCACACTGGGGAGAAACCCTATACATGCTTGGAGTGTGGACAGAGCTTCA
CTTTTAATGGAAATCTACGTAGACATCAAAAGATTCACACTGGGGAGAAGCCCTATAAATGCTTGGAGTGTGGACAGAGC
TTCATTGAAAGTTCAACTCTAAGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCTTGGAGTGTGGACA
GAGCTTCATTGATAGTTCAACTCTAAGTTCACATCAGAGGACTCACACTGAGGAGAAACCCTATAAATGCTTGGAGTGTG
GACTGAGCTACAAGCGGAGTTCAGATCTACTCTCACATTTAAGGACTCACACTGGAGAGAAACCTTACACATGCCTGGAG
TGTGGACAGAGCTTCACTTGGAGTTCAGGTCTACGATCACATCAAAGGACTCACACTGGAGAGAAATCCTATACATGCCT
GGAGTGTGGACAGAGCTTCACTCATAGTTCAAACCTTCATTCACATCAAAGGACTCACACTGGGGAGAAACCCTGTAAAC
CCTATAAATGCTCAGAGTGCGGAAAAAGCTACGCCCGGAGTGAAAATCTACGTTTACATCAAAGGATTCACACAGGGGAG
AAACCTTATAAATGCCTGGAGTGTGGAAAGAGCTTCTCTATTAAAGGAAGTCTACGTAGACATCAGAGGACTCACACTGT
CCAAGCAGGCACATCAGATGTCCTCAGAGACATCTTCCCGCCTCTCCTATCCAATCCAGCCGGCACAGGCCCAGCAGATC
CCATCCTTCTTGGAATCTCACCAGGAGATAATGTTGGACAGAGAGCTTCAGGATTTGACACTCATACCATGAACCAAGTG
CGACATGAATCAGGTGCGACACAGGCCTGGGCTGTGGCGCAGGCTGGAGAGCAGCCAGTTGCAGCCAGCTGCAATGAATC
ACTCTGA

Alignment

ORF - retro_acar_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.58 %
• Parental protein coverage: 65.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKPYNCLECGQSFADSSTLRKHQRTHTGEKPYKCLECGQNFSHNSQLHRHQRTHTGEKPYNCLECGQSFA
          .K....L.CG..F.....L..H...HTG...Y.C.ECG.NF.HNS.LH..Q..HTGEKPY.CLECGQS..
Retrocopy DKASKALQCGKCFTRRAHLQQHEKIHTGDEHYECMECGNNFTHNSNLH--QNSHTGEKPYTCLECGQSYT

Parental  RSSVLRSHQRTHTGEKPYKCLECGHSFADSSTLRKHQRTHTGEKPYNCLECGQSFTQKGHLHTHQRTHTG
          R...L.SH.RTHTGEKPY.CLECG.SFA.S..LR.HQRTHTG.KPY.CLECGQ.FT..G.L..HQRTHTG
Retrocopy RIANLHSHERTHTGEKPYTCLECGKSFAQSVHLRSHQRTHTGKKPYKCLECGQNFTNNGNLRRHQRTHTG

Parental  EKPYKCLECGQSFAHSSGLRNHQRTHTGEKPYNCLECGQSFADSTGLRSHQRTHTGEKPYNCLECGQSFT
          EKPYKCLECGQSF..SS.LR.HQRTHTGEKPY.CLECGQSF.DS..LRSHQRTHTGEKPY.CLECG.S.T
Retrocopy EKPYKCLECGQSFTDSSSLRSHQRTHTGEKPYKCLECGQSFTDSSSLRSHQRTHTGEKPYKCLECGLSYT

Parental  QKGHFHTHQRTHTGEKPYNCMECGQSFTQKGHLHTHQRTHTGEKPYNCLECGQSFTQNSGLRTHQRTHTG
          .......H.RTHTGEKPY.C.ECGQSF.....L..HQRTHTGEKPYNCLECGQSFT..S.LR.HQRTHTG
Retrocopy RSASLYSHLRTHTGEKPYTCLECGQSFILSSSLYSHQRTHTGEKPYNCLECGQSFTHSSTLRKHQRTHTG

Parental  EKPYKCLECGQSFTQKGNLHKHQRTHTGEKPYKCLECGHSFARSSHLRSHHERTHTGEKPYKCLECGQSF
          EKPY.CLECGQSFT..GNL..HQ..HTGEKPYKCLECG.SF..SS.L.SH..RTHTGEKPYKCLECGQSF
Retrocopy EKPYTCLECGQSFTFNGNLRRHQKIHTGEKPYKCLECGQSFIESSTLSSH-QRTHTGEKPYKCLECGQSF

Parental  TQTSGLHRHQRTHTGEKPYKCLECGQSFTHSSGLRSHQRTHTGEKPYKCLECGQTFTHSSGLRSHQRTHT
          ...S.L..HQRTHT.EKPYKCLECG.S...SS.L.SH.RTHTGEKPY.CLECGQ.FT.SSGLRSHQRTHT
Retrocopy IDSSTLSSHQRTHTEEKPYKCLECGLSYKRSSDLLSHLRTHTGEKPYTCLECGQSFTWSSGLRSHQRTHT

Parental  GDKSYTCLECGQSYTRSSSLRSHQRTHTGEKP---YTCLECGQSFTRSSGLRRHQRTHTGEKPYNCLECG
          G.KSYTCLECGQS.T.SS.L.SHQRTHTGEKP...Y.C.ECG.S..RS..LR.HQR.HTGEKPY.CLECG
Retrocopy GEKSYTCLECGQSFTHSSNLHSHQRTHTGEKPCKPYKCSECGKSYARSENLRLHQRIHTGEKPYKCLECG

Parental  QSFTQKGHLHSHQRTHT
          .SF..KG.L..HQRTHT
Retrocopy KSFSIKGSLRRHQRTHT

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	1.25 RPM	0.53 RPM
SRP009831_brain	0.66 RPM	0.47 RPM
SRP009831_dewlap	1.39 RPM	0.76 RPM
SRP009831_embryo	2.49 RPM	0.65 RPM
SRP009831_heart	1.09 RPM	0.57 RPM
SRP009831_liver	0.41 RPM	0.04 RPM
SRP009831_lung	0.86 RPM	0.05 RPM
SRP009831_ovary	2.12 RPM	1.00 RPM
SRP009831_skeletal_muscle	0.07 RPM	0.04 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_34 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_34 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34 ,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248,