RetrogeneDB ID: retro_ecab_952

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:30841955..30842306(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL13
• Ensembl ID: ENSECAG00000021161
• Aliases: None
• Description: mitochondrial ribosomal protein L13 [Source:HGNC Symbol;Acc:14278]

Sequence

>retro_ecab_952
GATCATGTTGTCATAATGAACACAAGGCACATTGCATTTTCTGGAAACAAATGGGAACAAAAGGTGTATTCCTCACATAC
TGGCTACCCAGGTGGATTGAAACAAGTAACAGCTGCTCAACTTCACCAGAAGGATCCAGTGGCAATTGTAAAACTGGCTA
TTTATGGCATGCTGCCAAAAAACCTTCACAGAACTATGATGCAGAGGTTGCATCTTTTCCCAGATGAAGACATACCAGAA
GATATTCTTAAGAATTTAGTGGAAGAGCTTCCTTAACCTCGGAAAGTACCCAGACGTCTAGATGAGTGCACACAAGAAGA
AATAGAGGCTTTCCCAAGAGTGTGGTCCCCA

Alignment

ORF - retro_ecab_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.61 %
• Parental protein coverage: 68.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGFKQVTAAQLHQKDPVAIVKLAIYGMLPKNLHRRTMMQR
          DHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGG.KQVTAAQLHQKDPVAIVKLAIYGMLPKNLH.RTMMQR
Retrocopy DHVVIMNTRHIAFSGNKWEQKVYSSHTGYPGGLKQVTAAQLHQKDPVAIVKLAIYGMLPKNLH-RTMMQR

Parental  LHLFPDEDIPEDILKNLVEELPQPRKVPRRLDEYTQEEIEAFPRVWSP
          LHLFPDEDIPEDILKNLVEELP.PRKVPRRLDE.TQEEIEAFPRVWSP
Retrocopy LHLFPDEDIPEDILKNLVEELP*PRKVPRRLDECTQEEIEAFPRVWSP

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	3.25 RPM
SRP021940_cerebellum	0.10 RPM	4.67 RPM
SRP021940_embryo	0.20 RPM	6.11 RPM
SRP021940_placental_villous	0.05 RPM	4.52 RPM
SRP021940_synovial_membrane	0.08 RPM	4.17 RPM
SRP021940_testis	0.13 RPM	5.31 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_952 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_952 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952 ,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274, retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,