RetrogeneDB ID: retro_ecab_805

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:30197081..30197935(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC2
• Ensembl ID: ENSECAG00000015835
• Aliases: None
• Description: 5'-nucleotidase domain containing 2 [Source:HGNC Symbol;Acc:25717]

Sequence

>retro_ecab_805
GACCTGTATGGGGGCACCCACTCCCACTGTGGCAGATAGGCGGTTCCAACAGCAGAAGTCCCTCCATCAAGCAGTTCGTA
GATATGTCCTCGCTGCCGGAGACGGCACCGCTCTCCCAAGTGGTGGACCGCTTCCTGGGCCACAACCTGGAGTTTGACCA
CGCTTGCCTCTACAAGAGTGAGACAGATGCCGTTGGAGACGTGCACGTGAAGGGCCTCAAATACGAGTGGATCCAGTGGG
ACAGGGAGAAGTACATCTCCAAAGTGGAGGAAATATTCGCCGTCTTGAGCGCCTGGTCCATGGGAAACAGCTGGCCTCAT
CACCAACGGTGTTTTCTGCTTCGTGACAGGGGGATGTGGCACGTGGCGGATCACCACTGGCGTTGACTCTTCAAGGAAGT
CATTATACAGGCAGATAAGCCCAGACTTTTCACCTACTGGCGCAAGCCGTTCAGAAACCTCGATTAGAAGGGCTCACTCG
TGTGAGACTGTATCAGCGCCCTGGACAAGGGCGCGATCTATCGGCAGGGAAACCTTTTGGACTTCCTGTGCCTGATGGAA
TGGTGCGGTCTCTGCAAGTTGTCCTTCAGAAACCGCCTCTACAGTGACCTGGCGGAACTCCTGCTGCCGCACACCTGGCG
TGAGGGCATCATCATCCCCAAGCTGGAGTGCAAGACGCGCATCATCAACGCAGTGCAGAACCCGCACTCACTGACTCAGC
AGCGGCGTTCACCAGACTGCTTAGAGCACAGGCAGACCTTCCAGGACACAGAATCGCAGCAGATGCGGGGTGCCTGGATG
AAGGCATGAAAGGAGCTGAGGTGAATCACCGAAGTCCTGTTCAACACTCAGTTT

Alignment

ORF - retro_ecab_805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.96 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DLYGGTQH-IPLYQMSGFYGKGPSIKQFMDIFSLPEMALLSCVVDYFLGHSLEFDQAHLYKDVTDAIRDV
          DLYGGT.H..PL.Q..G.....PSIKQF.D..SLPE.A.LS.VVD.FLGH.LEFD.A.LYK..TDA..DV
Retrocopy DLYGGT-H<LPLWQIGGSNSRSPSIKQFVDMSSLPETAPLSQVVDRFLGHNLEFDHACLYKSETDAVGDV

Parental  HVKGLMYQWIEQDMEKYILREDETFAVLS-RLVAHGKQLF-LITNSPFSFV-DKGMRHMVGPDWRQLFDV
          HVKGL.Y.WI..D.EKYI....E.FAVLS.RLV.HGKQL..LITN..F.FV.D.GM.H.....WR.LF..
Retrocopy HVKGLKYEWIQWDREKYISKVEEIFAVLS<RLV-HGKQLA<LITNGVFCFV<DRGMWHVADHHWR*LFKE

Parental  VIVQADKPSFFTDRRKPFRKLDEKGSLQWDRITSLEKGKIYRQGNLFDFLRLTEWRGPRVLYFGDHLYSD
          VI.QADKP..FT..RKPFR.LD.KGSL..D.I..L.KG.IYRQGNL.DFL.L.EW.G...L.F...LYSD
Retrocopy VIIQADKPRLFTYWRKPFRNLD*KGSLV*DCISALDKGAIYRQGNLLDFLCLMEWCGLCKLSFRNRLYSD

Parental  LADLMLRHGWRTGAIIPELEREIRIINTEQYMHSLTWQQALTGLLERMQTYQDAESRQVLAAWMKERQEL
          LA.L.L.H.WR.G.IIP.LE...RIIN..Q..HSLT.Q......LE..QT.QD.ES.Q...AWMK...EL
Retrocopy LAELLLPHTWREGIIIPKLECKTRIINAVQNPHSLTQQRRSPDCLEHRQTFQDTESQQMRGAWMKA*KEL

Parental  RCITKALFNAQF
          R.IT..LFN.QF
Retrocopy R*ITEVLFNTQF

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	44.04 RPM
SRP021940_cerebellum	0.00 RPM	81.79 RPM
SRP021940_embryo	0.00 RPM	185.63 RPM
SRP021940_placental_villous	0.00 RPM	13.57 RPM
SRP021940_synovial_membrane	0.00 RPM	84.55 RPM
SRP021940_testis	0.26 RPM	41.18 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_805 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_805 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008538	1 retrocopy	retro_amel_278,
Canis familiaris	ENSCAFG00000009184	1 retrocopy	retro_cfam_418,
Equus caballus	ENSECAG00000015835	1 retrocopy	retro_ecab_805 ,
Myotis lucifugus	ENSMLUG00000015418	1 retrocopy	retro_mluc_1559,
Tursiops truncatus	ENSTTRG00000008562	1 retrocopy	retro_ttru_1120,