RetrogeneDB ID: retro_ecab_645

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 25:14212286..14212976(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPIA
• Ensembl ID: ENSECAG00000011754
• Aliases: None
• Description: ribose 5-phosphate isomerase A [Source:HGNC Symbol;Acc:10297]

Sequence

>retro_ecab_645
AAGAAGCTGGCGGGCCGCGCGGCCATGGAGAACCACGTGAGGAATAACCAAGTACTGGGAATTGGAAGTGGTTCTACAAT
TGTCCCTGCTGTGCAACGAATAGCTGAAAGAGTGAAACAAGAGAATCTGAACCTCGTCTGTATTCCCACGTCCTTCCAGG
CCCGTCAGCTCATCCTGCAATACGGCTTAATTCTCAGTGACCTGGACCGACATGCAGAGATGGACCTTGCCATTGATGGT
GCTAATGAAGTAGATGCTGACCTCAGTCTCATCAAGGGCGGTGGAGACTGCCTGACCCAGGAGAAAATTGTGGCTGGCTA
TGCCAGTCGCTTCATTGTGATTGCTGATTTCAGGAAAGATTCAAAGAACCTTGGGGATCAATGGCACAAAGGAATCCCCA
CCGAGGTCATCCCAATGGCCCGTGTCCCAGTGAGGCGAGCTGTGACCTAGAAGTTTGGGGGCGCGATTGAACTTCAAATG
GCCATCAAAAAGGCAGGTCCTGTGGTGACAGATAATGGGAATTTTATCCTGGACTGGAAGTTTGACGGGGTACACAAATG
GAGTGAAGTGAACACAGCTATCAAAATGATCCCAGGCGTGGTGGATACAGGCCTATTCAACAACATGGCTGAGAGAGTTT
ATTTCGGGTTGCAGGACGGCTCAATGAACATGAGGGAGAGGCCTTTCTGT

Alignment

ORF - retro_ecab_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.3 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKLAGRAAVENHVRNNQVLGIGSGSTIVHAVQRIAERVKQENLNLVCIPTSFQARQLILQYGLTLSDLDR
          KKLAGRAA.ENHVRNNQVLGIGSGSTIV.AVQRIAERVKQENLNLVCIPTSFQARQLILQYGL.LSDLDR
Retrocopy KKLAGRAAMENHVRNNQVLGIGSGSTIVPAVQRIAERVKQENLNLVCIPTSFQARQLILQYGLILSDLDR

Parental  HPEIDLAIDGADEVDADLNLIKGGGGCLTQEKIVAGYASRFIVIADFRKDSKNLGDQWHKGIPIEVIPMA
          H.E.DLAIDGA.EVDADL.LIKGGG.CLTQEKIVAGYASRFIVIADFRKDSKNLGDQWHKGIP.EVIPMA
Retrocopy HAEMDLAIDGANEVDADLSLIKGGGDCLTQEKIVAGYASRFIVIADFRKDSKNLGDQWHKGIPTEVIPMA

Parental  YVPVSRAVTRKFGGTIELRMAINKAGPVVTDNGNFILDWKFDRVHKWSEVNTAIKMIPGVVDTGLFINMA
          .VPV.RAVT.KFGG.IEL.MAI.KAGPVVTDNGNFILDWKFD.VHKWSEVNTAIKMIPGVVDTGLF.NMA
Retrocopy RVPVRRAVT*KFGGAIELQMAIKKAGPVVTDNGNFILDWKFDGVHKWSEVNTAIKMIPGVVDTGLFNNMA

Parental  ERVYFGMQDGSVNMREKPFC
          ERVYFG.QDGS.NMRE.PFC
Retrocopy ERVYFGLQDGSMNMRERPFC

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	0.00 RPM	5.04 RPM
SRP021940_embryo	0.18 RPM	17.95 RPM
SRP021940_placental_villous	0.00 RPM	13.04 RPM
SRP021940_synovial_membrane	0.05 RPM	9.99 RPM
SRP021940_testis	0.06 RPM	20.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_645 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_645 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002866	1 retrocopy	retro_btau_1373,
Equus caballus	ENSECAG00000011754	1 retrocopy	retro_ecab_645 ,
Macropus eugenii	ENSMEUG00000008256	1 retrocopy	retro_meug_1506,
Microcebus murinus	ENSMICG00000006462	1 retrocopy	retro_mmur_722,
Myotis lucifugus	ENSMLUG00000005384	1 retrocopy	retro_mluc_1129,
Monodelphis domestica	ENSMODG00000009649	1 retrocopy	retro_mdom_320,
Oryctolagus cuniculus	ENSOCUG00000006840	3 retrocopies	retro_ocun_1541, retro_ocun_1708, retro_ocun_1709,
Otolemur garnettii	ENSOGAG00000034178	2 retrocopies	retro_ogar_1218, retro_ogar_518,
Tarsius syrichta	ENSTSYG00000006406	8 retrocopies	retro_tsyr_1081, retro_tsyr_1088, retro_tsyr_1902, retro_tsyr_2028, retro_tsyr_393, retro_tsyr_709, retro_tsyr_725, retro_tsyr_994,
Tursiops truncatus	ENSTTRG00000000876	2 retrocopies	retro_ttru_1175, retro_ttru_799,