RetrogeneDB ID: retro_ecab_490

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:51964391..51964818(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSECAG00000021662
• Aliases: None
• Description: stathmin 1 [Source:HGNC Symbol;Acc:6510]

Sequence

>retro_ecab_490
ACTTCTGATATTCAAATGAAAGTCTGAAGAAGTGTCCCTCAGGCCAGGCTTCTGAGCAGTTTCTCAGTCCTTGGTCAAAA
GAATCCATCCCAGCATTCTCCCTTTCACCTCCAAAGAAGAGTCTTTCCCTGCAGGAAATTCAGAAGAAATTAGAAGCCGC
AAAAGAAAGACACAAGTCCCAAGAAGGTGAGGTCTTGAAGCAGCTTGCTGAGAAAGGAGAGCACCAGAAACAAATGTTTC
AGAAAGCAGTAGAAGAGAACACAACTTCAGTAAAATGGCAGAAGAGGAGCTGACCCACAAAATGGAAGAGAACCAAGAGG
CACAGATGGATTCCAAGCTGGAGCACGTGTGAGAGAAAGACAAGCACGTGGAAGAAGCATGGGAGAAGCATGAATTCAAA
GACCCTGCCGATGAGACTGAGGCTGAC

Alignment

ORF - retro_ecab_490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.13 %
• Parental protein coverage: 98.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSDIQVK-ELEKRASGQAFELILSPRSKESVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQ
          .SDIQ.K..L.K..SGQA.E..LSP.SKES.P.F.LSPPKK..LSL.EIQKKLEAA.ER.KS.E.EVLKQ
Retrocopy TSDIQMK<SLKKCPSGQASEQFLSPWSKESIPAFSLSPPKKS-LSLQEIQKKLEAAKERHKSQEGEVLKQ

Parental  LAEKREHEKEVLQKAIEEN-NNFSKMAEEKLTHKMEANKENREAQMAAKLERLREKDKHIEEVRKNKESK
          LAEK.EH.K...QKA.EEN..NFSKMAEE.LTHKME...EN.EAQM..KLE...EKDKH.EE.....E.K
Retrocopy LAEKGEHQKQMFQKAVEEN<HNFSKMAEEELTHKME---ENQEAQMDSKLEHV*EKDKHVEEAWEKHEFK

Parental  DPADETEAD
          DPADETEAD
Retrocopy DPADETEAD

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	0.12 RPM	2.42 RPM
SRP021940_cerebellum	0.00 RPM	64.60 RPM
SRP021940_embryo	0.05 RPM	377.73 RPM
SRP021940_placental_villous	0.00 RPM	36.23 RPM
SRP021940_synovial_membrane	0.08 RPM	22.48 RPM
SRP021940_testis	0.06 RPM	294.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_490 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_490 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490 ,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271, retro_sara_764,