RetrogeneDB ID: retro_ecab_229

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:10575519..10576010(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000023767
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TXN2
• Ensembl ID: ENSECAG00000013929
• Aliases: None
• Description: thioredoxin 2 [Source:HGNC Symbol;Acc:17772]

Sequence

>retro_ecab_229
ATGGCTCAGCAACTTCTGCTGAGGAGGTGCCTGGCCTCTGTCACCTCCAGGAAGCCCCTCAGAGTCAGTGGGCACCCCTC
ACCTCCAGGGCCCAGCAGACTGCACAGTGCAGTCCTCATGGCTTGATAGTAACCCTGGCTCCAGCCTGGTTAATATACAC
CACCAGAGTCTCTACAATGACCTTTAACGTCCAGAGTGGACCTGAGTTTCAAGACCGAGTTATCAACAGTGAGTCACCAG
TGGTGGCAGATTTCCATGCACAGTGGTGGGGCCCCTGCAGGATCCTGGGACCGAGGTTAGAGAAGATGGTGGCCAAGCAG
CACGGAAAGGTGGTGATGGCCAAGGTGGATACTGATGGCCACACAGACTTCGCTATGGAATATGAAGTGTTGGCTCTTCC
CACTGTGCCAGCCATCAAGAATGGGGACGTGGTGGACAAGTTTGTGGGCTTCAAGGACCAGCTGGAGGCCTCCCTGAAGA
AGCCGATTGGC

Alignment

ORF - retro_ecab_229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQRLLLRRFLASVVSRRPC-PGRWGPLTSRALPAPQCGPGDLTGTPSQARSLYTTRVCATTFNIQDGPD
          MAQ.LLLRR.LASV.SR.P.....W.PLTSRA....QC.P..L..T...A...YTTRV...TFN.Q.GP.
Retrocopy MAQQLLLRRCLASVTSRKPL<QSQWAPLTSRAQQTAQCSPHGLIVTLAPAWLIYTTRVSTMTFNVQSGPE

Parental  FQDRVVNSETPVVVDFHAQWCGPCKILGPRLEKMVAKQHGKVVMAKVDIDDHTDLAIEYEVSAVPTVLAM
          FQDRV.NSE.PVV.DFHAQW.GPC.ILGPRLEKMVAKQHGKVVMAKVD.D.HTD.A.EYEV.A.PTV.A.
Retrocopy FQDRVINSESPVVADFHAQWWGPCRILGPRLEKMVAKQHGKVVMAKVDTDGHTDFAMEYEVLALPTVPAI

Parental  KNGDVVDKFVGIKDEDQLEAFLRKLIG
          KNGDVVDKFVG.K..DQLEA.L.K.IG
Retrocopy KNGDVVDKFVGFK--DQLEASLKKPIG

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	33.23 RPM
SRP021940_cerebellum	0.00 RPM	77.28 RPM
SRP021940_embryo	0.03 RPM	62.78 RPM
SRP021940_placental_villous	0.00 RPM	44.50 RPM
SRP021940_synovial_membrane	0.00 RPM	43.51 RPM
SRP021940_testis	0.00 RPM	74.75 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_229 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_229 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000013929	1 retrocopy	retro_ecab_229 ,
Erinaceus europaeus	ENSEEUG00000010654	2 retrocopies	retro_eeur_554, retro_eeur_67,
Homo sapiens	ENSG00000100348	1 retrocopy	retro_hsap_179,
Gorilla gorilla	ENSGGOG00000028091	1 retrocopy	retro_ggor_260,
Myotis lucifugus	ENSMLUG00000015841	1 retrocopy	retro_mluc_483,
Monodelphis domestica	ENSMODG00000000837	2 retrocopies	retro_mdom_1125, retro_mdom_13,
Pteropus vampyrus	ENSPVAG00000002012	1 retrocopy	retro_pvam_1431,
Sarcophilus harrisii	ENSSHAG00000000670	1 retrocopy	retro_shar_61,
Tursiops truncatus	ENSTTRG00000006612	1 retrocopy	retro_ttru_438,