RetrogeneDB ID: retro_ecab_113

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:181175942..181176584(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004957
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSECAG00000017154
• Aliases: None
• Description: ribosomal protein L10 [Source:HGNC Symbol;Acc:10298]

Sequence

>retro_ecab_113
ATGGGCCGCCGCCCCGCTCGCTGTTACCGCTACTGTAAGAACAAGCCTTACCCAAAGTCTCGCTTCTGCCGCGCGGTCCC
CGATGCCAAGATCCGCATCTTCGACCTGGGCCGGAAGAAGGCCAAAGTGGACGAGTTCCCGCTCTGTGGGCACATGGTGT
CTGATGAACACGAGCAGCTCTCCTCCGAGGCCCTGGAGGCCGCGCGCATCTGTGCCAACAAGTACTTGGTGAAAAGCTGC
GGCCGCGACGGCTTTCACCTCCGCGTGCGGCTCCACCCCTTCCACGTCATCCGCATCAACAAGATGATGGCCTGTGCTGG
GGCCGACAGGCTCCAAACCGGCATGCGGGGGGCCTTCGGAAAGCCCCAGGGCACGGTGGCCAGAGTCTGCATCGGCCAGA
TCATCATGTCCATCCGCACCAAGCTTCAGAACAAGGAGCACGTGGTGGAAGCCTTACGCAGGGCCAAGTTCAAGTTCCCC
GGCCGCCAGAAGATCCACGTCTCCAAGAAGTGGGGCTTTACCAAGTTTAATGCCCATAAATTTGATGACAAGGTGGCCGA
GAAGCGCCTCATCCCGGATGGTTGTGGAGTCAAATACGTGCCCAGTCGTGGCCCCCTGGCCCCGTGGCGAGCTCTGTACT
CA

Alignment

ORF - retro_ecab_113 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPARCYRYCKNKPYPKSRFCR.VPDAKIRIFDLGRKKAKVDEFPLCGHMVSDE.EQLSSEALEAARI
Retrocopy MGRRPARCYRYCKNKPYPKSRFCRAVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEHEQLSSEALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CANKY.VKSCG.DGFH.RVRLHPFHVIRINKM..CAGADRLQTGMRGAFGKPQGTVARV.IGQ.IMSIRT
Retrocopy CANKYLVKSCGRDGFHLRVRLHPFHVIRINKMMACAGADRLQTGMRGAFGKPQGTVARVCIGQIIMSIRT

Parental  KLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHV.EALRRAKFKFPGRQKIH.SKKWGFTKFNA..F.D.VAEKRLIPDGCGVKY.P.RGPL..WR
Retrocopy KLQNKEHVVEALRRAKFKFPGRQKIHVSKKWGFTKFNAHKFDDKVAEKRLIPDGCGVKYVPSRGPLAPWR

Parental  ALHS
          AL.S
Retrocopy ALYS

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	1464.71 RPM
SRP021940_cerebellum	0.05 RPM	470.04 RPM
SRP021940_embryo	0.05 RPM	1043.21 RPM
SRP021940_placental_villous	0.29 RPM	768.00 RPM
SRP021940_synovial_membrane	0.16 RPM	1252.86 RPM
SRP021940_testis	3.33 RPM	264.98 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_113 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_113 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_113 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007454	2 retrocopies	retro_btau_140, retro_btau_99,
Cavia porcellus	ENSCPOG00000002355	1 retrocopy	retro_cpor_64,
Equus caballus	ENSECAG00000017154	1 retrocopy	retro_ecab_113 ,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Microcebus murinus	ENSMICG00000004658	2 retrocopies	retro_mmur_1077, retro_mmur_4,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Mustela putorius furo	ENSMPUG00000009320	3 retrocopies	retro_mputfur_1405, retro_mputfur_54, retro_mputfur_84,
Mus musculus	ENSMUSG00000008682	1 retrocopy	retro_mmus_71,
Otolemur garnettii	ENSOGAG00000000099	3 retrocopies	retro_ogar_293, retro_ogar_2995, retro_ogar_3284,
Ictidomys tridecemlineatus	ENSSTOG00000011857	2 retrocopies	retro_itri_174, retro_itri_506,