RetrogeneDB ID: retro_ecab_397

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 17:35126825..35127160(+)
• Located in intron of: ENSECAG00000019161

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSECAG00000024079
• Aliases: None
• Description: ribosomal protein L31 [Source:HGNC Symbol;Acc:10334]

Sequence

>retro_ecab_397
AGAAGGGTGGCGAGAAGGCCTGCCATCAACGAGATGGGGACCAGAGAATACATCATCAACATGCACAAGCTCAGCCATGG
AGTGGGCTTCAAAAAGCATGCCCCATAGGCTTTCAAAGAAATTGGAAATTTGCCATGAAGAAGACAGGAACTCCAGAAGT
ATGCATTGACACCAGGCTCAACAAAGCTGCCTGGGCCAAAGGAATAAGGAATGCCCCATACCATATCCATGTGTGGTTGT
CCAGAAAATGTAATGACGATGAAGATTCACCAAACAGACTCTATATGTTGGTTACCTATGTACCTGTCACCACCTTCAAA
AATCTACAGTCAATG

Alignment

ORF - retro_ecab_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.14 %
• Parental protein coverage: 92.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRVARRRRAAAINEVVTREYTINIHKRIHGVGFKKRAPRALKEIR-KFAMKEMGTPDVRIDTRLNKAVWA
          RRVARR....AINE..TREY.IN.HK..HGVGFKK.AP.A.KEI..KFAMK..GTP.V.IDTRLNKA.WA
Retrocopy RRVARR---PAINEMGTREYIINMHKLSHGVGFKKHAP*AFKEIG<KFAMKKTGTPEVCIDTRLNKAAWA

Parental  KGIRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTV
          KGIRN.PY.I.V.LSRK.N.DEDSPN.LY.LVTYVPVTTFKNLQ..
Retrocopy KGIRNAPYHIHVWLSRKCNDDEDSPNRLYMLVTYVPVTTFKNLQSM

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
SRP021940_articular_cartilage	0.00 RPM	327.91 RPM
SRP021940_cerebellum	0.00 RPM	157.98 RPM
SRP021940_embryo	0.13 RPM	312.70 RPM
SRP021940_placental_villous	0.00 RPM	177.00 RPM
SRP021940_synovial_membrane	0.05 RPM	274.11 RPM
SRP021940_testis	0.13 RPM	148.80 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_397 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_397 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021031	5 retrocopies	retro_cpor_1184, retro_cpor_170, retro_cpor_190, retro_cpor_341, retro_cpor_366,
Equus caballus	ENSECAG00000024079	13 retrocopies	retro_ecab_1034, retro_ecab_1102, retro_ecab_163, retro_ecab_206, retro_ecab_259, retro_ecab_332, retro_ecab_397 , retro_ecab_414, retro_ecab_448, retro_ecab_451, retro_ecab_499, retro_ecab_812, retro_ecab_972,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94,
Loxodonta africana	ENSLAFG00000027873	12 retrocopies	retro_lafr_118, retro_lafr_187, retro_lafr_20, retro_lafr_245, retro_lafr_307, retro_lafr_56, retro_lafr_663, retro_lafr_703, retro_lafr_710, retro_lafr_778, retro_lafr_885, retro_lafr_926,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Mustela putorius furo	ENSMPUG00000012197	2 retrocopies	retro_mputfur_50, retro_mputfur_71,
Otolemur garnettii	ENSOGAG00000014494	10 retrocopies	retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Pongo abelii	ENSPPYG00000025870	4 retrocopies	retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Sus scrofa	ENSSSCG00000008170	4 retrocopies	retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263,
Sus scrofa	ENSSSCG00000025180	6 retrocopies	retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,