RetrogeneDB ID: retro_ecab_864

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:71703327..71703927(-)
• Located in intron of: ENSECAG00000014091

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMZ2
• Ensembl ID: ENSECAG00000011450
• Aliases: None
• Description: archaelysin family metallopeptidase 2 [Source:HGNC Symbol;Acc:28041]

Sequence

>retro_ecab_864
CAGTTCTTAAAAGAGAAGAAACCTAAAGATGCCTTCTGTGTTGTGGGAAAACAATGGTTGAGCTTTACCAAAGAGACCAC
TAGAATTTTGTCTTTGAACACACCCCTTTGACAGATGGTGTGGGGATATTAGCTTTGCCGCGTATGGCAATTTTTATAGC
TCATGCTATGAAGGCAAAGTAAAGAAGCTGCAGAAAATATCTTCAAGTGACTCTTCGATTTTTGATAAGTATTACATTCC
TGAAGTGACTAGTGTTTTGCTGCTTCGATCCTGTAAGACTTGACCTATGAGATTGGACACAGATTTGGACTTTGACACTG
CCAGTGGCTTGCATGCCTAACATAAGGCTTCAGCCACTTGGAAGAAGCTGCCTGGAGCCCCCTAAACCTTTGTCCTATCT
GTTTACACAAGTTGCAGTGTGCTATTGGTTTCAACCTTACAGAAAGATAGAAAGTGCTGGTGAGGTAGATTGACAAACCT
GCTGACAAAGCTGGAGTCCCTGAGAAACGTAGTGAGGATAATGTGAATTTGCCAAAACCTGTTGAAGCCTTTAAGGAATG
GAAAGAATGGATAATAAAATGCCTTGCTGTTCTCTAAAAA

Alignment

ORF - retro_ecab_864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.95 %
• Parental protein coverage: 56.67 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFLKKKKPGDAFCIVGV-TMIDLYPRDSWNFVFGQASLTDGVGIF-SFARYGSDFYSSRYEGRVKKPQKV
          .FLK.KKP.DAFC.VG..TM..LY.RD..NFVF....LTDGVGI..SFA.YG..FYSS.YEG.VKK.QK.
Retrocopy QFLKEKKPKDAFCVVGK<TMVELYQRDH*NFVFEHTPLTDGVGIL<SFAAYGN-FYSSCYEGKVKKLQKI

Parental  SSSDYSVFDNYYIPEVTSVLLLRSCKT-LTHEIGHIFGLRHCQWLACLMQGSNHLEEADRRPLNLCPICL
          SSSD.S.FD.YYIPEVTSVLLLRSCKT.LT.EIGH.FGL.HCQWLACL..G..HLEEA...PLNLCPICL
Retrocopy SSSDSSIFDKYYIPEVTSVLLLRSCKT<LTYEIGHRFGL*HCQWLACLT*GFSHLEEAAWSPLNLCPICL

Parental  RKLQCAIGFNIVERYKALVRWIDGASADTPRVTPKHSREDDVNLPKPVEAFKEWKEWIIKCLAVLRK
          .KLQCAIGFN..ER.K.LVR.ID...AD...V..K.S.ED.VNLPKPVEAFKEWKEWIIKCLAVL.K
Retrocopy HKLQCAIGFNLTER*KVLVR*ID-KPADKAGVPEKRS-EDNVNLPKPVEAFKEWKEWIIKCLAVL*K

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	20.90 RPM
SRP021940_cerebellum	0.00 RPM	29.96 RPM
SRP021940_embryo	0.00 RPM	17.90 RPM
SRP021940_placental_villous	0.00 RPM	10.92 RPM
SRP021940_synovial_membrane	0.00 RPM	13.07 RPM
SRP021940_testis	0.00 RPM	72.83 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_864 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_864 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009345	1 retrocopy	retro_btau_429,
Choloepus hoffmanni	ENSCHOG00000000493	1 retrocopy	retro_chof_2462,
Callithrix jacchus	ENSCJAG00000000254	1 retrocopy	retro_cjac_2798,
Cavia porcellus	ENSCPOG00000013061	1 retrocopy	retro_cpor_1226,
Equus caballus	ENSECAG00000011450	2 retrocopies	retro_ecab_440, retro_ecab_864 ,
Felis catus	ENSFCAG00000019195	1 retrocopy	retro_fcat_760,
Myotis lucifugus	ENSMLUG00000006771	2 retrocopies	retro_mluc_1540, retro_mluc_2056,
Mustela putorius furo	ENSMPUG00000014570	1 retrocopy	retro_mputfur_1224,