RetrogeneDB ID: retro_acar_115

Retrocopy location

• Organism: Anole lizard (Anolis carolinensis)
• Coordinates: 4:9321271..9322217(+)
• Located in intron of: ENSACAG00000003719

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP0
• Ensembl ID: ENSACAG00000003756
• Aliases: None
• Description: None

Sequence

>retro_acar_115
ATGCCCAGGGAAGACCGAGCCACGTGGAAATCCAACTATTTCCTCAAGATCATCCAACTCTTGGATGATTATCCAAAATG
CTTCATTGTGTGGGAGCAGACAACATGGATCCAAGCAGATGCAGCAGATCTGCATGTTCCTGCACGGGAAAGCTGTGGTC
CTCATGGGGAAGAACACCATGTTGCGCAAGGTCATCCGTGGGCATCTGGAGAACAACCCTGCTCTGGAGAAACTTTTGTC
TCATGTCCATTTCAACATGGGCTTTGTGTTGACCAAGGACAATCTGACTGAAATTTGAGACATGCTGTTGGCTAACAAAG
TGCCAGCTACTGCTCGTGTAAGTGTCATTGCCCCCTGCGATGTGACTGTGCCAGCCCAAAACACCGACCTGGGCCCTGAA
AAGACCTCCTTTTTCCAGGCTTTGGACATTACCACAAAGATTTCCAGAGGTACCATTGAAATCCTGATTGATGTGCAGTT
GATCAAGACTGGAGACAAAGTGGGTGCCAGCGAACCCACCTTGCTGAACATGCTGAACATCTCCCCCTTCTCCTTTGAGC
TCATCATCCAGCAGGTGTTTGATAACGGCAGCATTTATAACTCTAAAGTTCTGGACATCACCGAGGAGACCCTGTGAGGG
AGTTTCCTGGAGGGTGTCCGCAACGTTGCCAGCATCTGCTTGCAAATTGGCTACCCAGCCGTTGCCTCTGTGCCCCATTC
CATCATTAATGGGTACAAACGGGTCCTGGCTGTGGCTGTGGAAACCGACTACTCTTTCCCATTGGCTGAAAAGGTGAAGG
CCTTCCTGGCTGACCCATCAGCTTTTGTGGCTGCTGCCCCGGTTGCAGTGGAGACGGCTGACCCAGTCGCAGCTGCCCCG
GCTAAAGTGGAAGCCAAGGAAGAATCAGAAGAGTTGGACAAAGATATGGGATTTGGTCTCTTTGAC

Alignment

ORF - retro_acar_115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPREDRATWKSNYFLKIIQLLDDYPKCFIV-GADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHL
          MPREDRATWKSNYFLKIIQLLDDYPKCFIV.G....GSKQMQQI.M.L.GKAVVLMGKNTM.RK.IRGHL
Retrocopy MPREDRATWKSNYFLKIIQLLDDYPKCFIV>GSRQHGSKQMQQICMFLHGKAVVLMGKNTMLRKVIRGHL

Parental  ENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCDVTVPAQNTGLGPEKTSFFQ
          ENNPALEKLL.H...N.GFV.TK..LTEI.DMLLANKVPA.AR...IAPCDVTVPAQNT.LGPEKTSFFQ
Retrocopy ENNPALEKLLSHVHFNMGFVLTKDNLTEI*DMLLANKVPATARVSVIAPCDVTVPAQNTDLGPEKTSFFQ

Parental  ALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQVFDNGSIYNPEVLDITEE
          AL.ITTKISRGTIEIL.DVQLIKTGDKVGASE.TLLNMLNISPFSF.LIIQQVFDNGSIYN..VLDITEE
Retrocopy ALDITTKISRGTIEILIDVQLIKTGDKVGASEPTLLNMLNISPFSFELIIQQVFDNGSIYNSKVLDITEE

Parental  TLRGRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLAVAVETDYSFPLAEKVKAFLADPSAFVAAA
          TL.G.FLEGVRNVAS.CLQIGYP.VASVPHSIINGYKRVLAVAVETDYSFPLAEKVKAFLADPSAFVAAA
Retrocopy TL*GSFLEGVRNVASICLQIGYPAVASVPHSIINGYKRVLAVAVETDYSFPLAEKVKAFLADPSAFVAAA

Parental  PVAVETVAPVAAAPAKVEAKEESEESDEDMGFGLFD
          PVAVET..PVAAAPAKVEAKEESEE.D.DMGFGLFD
Retrocopy PVAVETADPVAAAPAKVEAKEESEELDKDMGFGLFD

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	0.00 RPM	895.88 RPM
SRP009831_brain	0.00 RPM	237.88 RPM
SRP009831_dewlap	0.00 RPM	417.90 RPM
SRP009831_embryo	0.00 RPM	1500.50 RPM
SRP009831_heart	0.10 RPM	914.17 RPM
SRP009831_liver	0.00 RPM	889.79 RPM
SRP009831_lung	0.00 RPM	635.91 RPM
SRP009831_ovary	0.04 RPM	248.21 RPM
SRP009831_skeletal_muscle	0.00 RPM	380.93 RPM

ChIP-Seq

Anolis carolinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_acar_115 retrocopy.

TSS

Anolis carolinensis was not studied using FANTOM5 data.

Lab

retro_acar_115 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 18 parental genes, and 71 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003756	2 retrocopies	retro_acar_111, retro_acar_115 ,
Ailuropoda melanoleuca	ENSAMEG00000005144	4 retrocopies	retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris	ENSCAFG00000010227	5 retrocopies	retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus	ENSECAG00000015816	2 retrocopies	retro_ecab_1090, retro_ecab_585,
Felis catus	ENSFCAG00000013354	1 retrocopy	retro_fcat_441,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii	ENSMEUG00000016409	12 retrocopies	retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672, retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166, retro_meug_294, retro_meug_772,
Myotis lucifugus	ENSMLUG00000001970	11 retrocopies	retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,