RetrogeneDB ID: retro_meug_1718

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold5476:25890..26251(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPC
• Ensembl ID: ENSMEUG00000009300
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide C [Source:HGNC Symbol;Acc:11157]

Sequence

>retro_meug_1718
CCATCTGTAAGTAGACATACTGCAGCTGGGGGAAACACAAAGAGAATGGGAGAAACTATTATCAGAAATGGATAGAAAAG
CAAGCCCAGAGCCTGACTGAAAAAACAACCACAGCATTTCAGCAAGCAAGAATTCCTCCCAATCTATTCTCAGCTCCTCC
ACTAGGAGGGTCTATGACACCACCTTCTCACACTAGCACAATGGGCACCCCGTTCCTGGAACGATGCCTTTGGGGCCTCC
TCCTGGCATGGGAATACCCATGAGAGGCCTCAGGCCCATGACACCTGGACCTCCAGTGATGAGACACCTTCCCCCTCCCA
CTATGGTGCCTACTCACCCAGCAATGCCCAGACCAGGCAGA

Alignment

ORF - retro_meug_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.88 %
• Parental protein coverage: 89.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSVRK-THCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAPPPGGAMIPPP-PSLPG
          PSV...T.CS..KHKEN...YYQKW.E.QAQSL..KTT.AFQQ..IPP..FSAPP.GG.M.PP...S..G
Retrocopy PSVSR<TYCSWGKHKENGRNYYQKWIEKQAQSLTEKTTTAFQQARIPPNLFSAPPLGGSMTPPSHTSTMG

Parental  PP-RPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGMRPPMGGHMP---MMPGPPMMRPPAR
          .P..PG.MP.....GPP..P.MG.P..G..P..P.P....P...H.P...M.P..P.M..P.R
Retrocopy TP<VPGTMPL----GPP--PGMGIPMRGLRPMTPGP----PVMRHLPPPTMVPTHPAMPRPGR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1718 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Macropus eugenii	ENSMEUG00000009300	1 retrocopy	retro_meug_1718 ,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Pongo abelii	ENSPPYG00000029902	3 retrocopies	retro_pabe_2367, retro_pabe_3397, retro_pabe_3524,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,