RetrogeneDB ID: retro_acar_3

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: AAWZ02037365:2507..4385(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSACAG00000026714
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_acar_3
GAATTAAATGTACATAGCACTGTTGACATGGAGGAGAAAGCATATAAATGTATCGAATGTGGAAAGAGCTTTAGTCAGCA
TGGAAAGCTGAAGAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTG
ATAGTTCAACTCTACGTAAACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAACTTC
TCTCATAATTCACAATTACATAGACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAG
CTTTGCTCGTAGTTCAGTTCTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGAC
ACAGCTTTGCTGATAGTTCAACTCTACGTAAACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGT
GGACAGAGCTTTGCTCGTAGTTCAGGTCTACGTTCACATCAAAGGACCCACACTGGGGAGAAACCCTATAAATGCCTGGA
GTGTGGACAGAGCTTTGCTCATAGTTCAGGACTACGTAACCATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCC
TGGAGTGTGGACAGAGCTTTGCTGATAGTACAGGACTACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAAA
TGCCTGGAGTGTGGACAGAGCTTTGCTGATAGTTCAACTCTACGTAAACATCAAAGGACTCACACTGGGGAGAAACCCTA
TAACTGCCTGGAGTGTGGACAGAGCTTCACTCAGAAGGGACACTTACATACACATCAAAGAACTCACACTGGGGAGAAAC
CCTATAAATGCCTGGAGTGTGGACAGAGCTTTGCTCATAGTTCAGGACTACGTAACCATCAAAGGACTCACACTGGGGAG
AAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTGATAGTACAGGACTACGTTCACATCAAAGGACTCACACTGG
GGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTCACTCAGAAGGGACACTTTCATACACATCAAAGGACTCACA
CTGGGGAGAAACCCTATAACTGCATGGAGTGTGGACAGAGCTTCACTCAGAAGGGACACTTACATACACATCAAAGAACT
CACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTCACTCAGAAGGGACACTTACATACACATCAAAG
AACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAACTTTGCTCATAGTTCAGGACTACGTACACATC
AAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAACTTTGCTCATAATTCAGTTCTACGTTCA
CATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAACTTTGCTCATAGTTCAGGACTACG
TACACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAGCTTTGCTCATAATTCAGTTC
TACGTTCACATCAAAGGACTCACACTGGGGAGAAACCCTATAACTGCCTGGAGTGTGGACAGAACTTTGCTCATAGTTCA
GGACTACGTACACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGTGGACAGAGCTTCACTCAGAA
GGGAAACTTACATAAACATCAAAGGACTCACACTGGGGAGAAACCCTATAAATGCCTGGAGTGCGGACATAGCTTCGCTC
GTAGTTCACATCTACGTTCACATCAAAGTTCACATCAA

Alignment

ORF - retro_acar_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.15 %
• Parental protein coverage: 79.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YKCIECGKSFSQHGKLKRHQRTHTGEKPYNCLECGQSFADSSTLRKHQRTHTGEKPYKCLECGQNFSHNS
          YKCIECGKSFSQHGKLKRHQRTHTGEKPYNCLECGQSFADSSTLRKHQRTHTGEKPYKCLECGQNFSHNS
Retrocopy YKCIECGKSFSQHGKLKRHQRTHTGEKPYNCLECGQSFADSSTLRKHQRTHTGEKPYKCLECGQNFSHNS

Parental  QLHRHQRTHTGEKPYNCLECGQSFARSSVLRSHQRTHTGEKPYKCLECGHSFADSSTLRKHQRTHTGEKP
          QLHRHQRTHTGEKPYNCLECGQSFARSSVLRSHQRTHTGEKPYKCLECGHSFADSSTLRKHQRTHTGEKP
Retrocopy QLHRHQRTHTGEKPYNCLECGQSFARSSVLRSHQRTHTGEKPYKCLECGHSFADSSTLRKHQRTHTGEKP

Parental  YNCLECGQSFTQKGHLHTHQRTHTGEKPYKCLECGQSFAHSSGLRNHQRTHTGEKPYNCLECGQSFADST
          YNCLECGQSF.....L..HQRTHTGEKPYKCLECGQSFAHSSGLRNHQRTHTGEKPYNCLECGQSFADST
Retrocopy YNCLECGQSFARSSGLRSHQRTHTGEKPYKCLECGQSFAHSSGLRNHQRTHTGEKPYNCLECGQSFADST

Parental  GLRSHQRTHTGEKPYNCLECGQSFTQKGHFHTHQRTHTGEKPYNCMECGQSFTQKGHLHTHQRTHTGEKP
          GLRSHQRTHTGEKPY.CLECGQSF........HQRTHTGEKPYNC.ECGQSFTQKGHLHTHQRTHTGEKP
Retrocopy GLRSHQRTHTGEKPYKCLECGQSFADSSTLRKHQRTHTGEKPYNCLECGQSFTQKGHLHTHQRTHTGEKP

Parental  YNCLECGQSFTQNSGLRTHQRTHTGEKPYKCLECGQSFTQKGNLHKHQRTHTGEKPYKCLECGHSFARSS
          Y.CLECGQSF...SGLR.HQRTHTGEKPY.CLECGQSF.....L..HQRTHTGEKPY.CLECG.SF....
Retrocopy YKCLECGQSFAHSSGLRNHQRTHTGEKPYNCLECGQSFADSTGLRSHQRTHTGEKPYNCLECGQSFTQKG

Parental  HLRSHHERTHTGEKPYKCLECGQSFTQTSGLHRHQRTHTGEKPYKCLECGQSFTHSSGLRSHQRTHTGEK
          H....H.RTHTGEKPY.C.ECGQSFTQ...LH.HQRTHTGEKPY.CLECGQSFT....L..HQRTHTGEK
Retrocopy HFHT-HQRTHTGEKPYNCMECGQSFTQKGHLHTHQRTHTGEKPYNCLECGQSFTQKGHLHTHQRTHTGEK

Parental  PYKCLECGQTFTHSSGLRSHQRTHTGDKSYTCLECGQSYTRSSSLRSHQRTHTGEKPYTCLECGQSFTRS
          PY.CLECGQ.F.HSSGLR.HQRTHTG.K.Y.CLECGQ.....S.LRSHQRTHTGEKPY.CLECGQ.F..S
Retrocopy PYNCLECGQNFAHSSGLRTHQRTHTGEKPYNCLECGQNFAHNSVLRSHQRTHTGEKPYNCLECGQNFAHS

Parental  SGLRRHQRTHTGEKPYNCLECGQSFTQKGHLHSHQRTHTGEKPFKCLECGQSFTHSSGLRRHQRTHTGEK
          SGLR.HQRTHTGEKPYNCLECGQSF.....L.SHQRTHTGEKP..CLECGQ.F.HSSGLR.HQRTHTGEK
Retrocopy SGLRTHQRTHTGEKPYNCLECGQSFAHNSVLRSHQRTHTGEKPYNCLECGQNFAHSSGLRTHQRTHTGEK

Parental  PYNCLECGQGFADSPGLHSHQRTHTGEKPYKCLECGQSFTHSSVLRSHQRTH
          PY.CLECGQ.F.....LH.HQRTHTGEKPYKCLECG.SF..SS.LRSHQ..H
Retrocopy PYKCLECGQSFTQKGNLHKHQRTHTGEKPYKCLECGHSFARSSHLRSHQSSH

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	0.56 RPM	0.53 RPM
SRP009831_brain	1.56 RPM	0.47 RPM
SRP009831_dewlap	3.16 RPM	0.76 RPM
SRP009831_embryo	1.30 RPM	0.65 RPM
SRP009831_heart	0.57 RPM	0.57 RPM
SRP009831_liver	0.37 RPM	0.04 RPM
SRP009831_lung	0.65 RPM	0.05 RPM
SRP009831_ovary	2.59 RPM	1.00 RPM
SRP009831_skeletal_muscle	0.22 RPM	0.04 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_3 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_3 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,