RetrogeneDB ID: retro_ecab_440

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:2895304..2895942(-)
• Located in intron of: None

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_440
GGATCTCTAGGGAACACTAGAATTACCAGTGAAGAATATATTGAATGGCACCAGGTTAATTATGCAGCATTTTTCTATGG
CTTGACACTAAAACTCCTAGAACCACATCGTGGTTTGGCAATGAAGTGTTCCTTTAGAGTCAACGACAACACACAAAACC
TACAAATTCATGCAGGGCACATCTTGACGTTTTCAAAAAGGAAGAAACATGAAGATGCATTCTGTGTTGTGGGGATAACA
ATGACTGATCTTTACTCAAGAGGCTCCTGGGATTCTTCCTCCGGACAGGCCTCGTTGACAGATGGTGTGCAAATATCAGC
TTTGCCACAGATGGCAGTAATTTTTATAGCTCATGATATGCAGACAAAGTGAAGGTGCTCCAGAAAACATCTTCAATTGA
CTATTCAATTTTTGATAAATATTATATTCCTGCAATGACTAGTATTTTGCTGCTTCAATCCTGTAGGATTTTAACCTATG
AGATTGAACACATACTTAGACTGCAACATTGTCAGGGGCCTACATGCCTAATGCAAGGCTCCAGCCACTTGGAAGAAGTT
AACCATCACCCTCTGAACCTTCGGCCTATCCATTTATGCAAGTTGCACTGTGCTAGTGGCTTCAACATATCGCAGAAA

Alignment

ORF - retro_ecab_440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.42 %
• Parental protein coverage: 59.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSLGNTRAISEEYIKWLQGYCEAFFYGLTVKLLAPVPVSATRCSFRVNDSTQNLQIHAGHILKFLKKKKP
          GSLGNTR..SEEYI.W.Q....AFFYGLT.KLL.P....A..CSFRVND.TQNLQIHAGHIL.F.K.KK.
Retrocopy GSLGNTRITSEEYIEWHQVNYAAFFYGLTLKLLEPHRGLAMKCSFRVNDNTQNLQIHAGHILTFSKRKKH

Parental  GDAFCIVGVTMIDLYPRDSWNFVFGQASLTDGVGI-FSFARYGSDFYSSRYEGRVKKPQKVSSSDYSVFD
          .DAFC.VG.TM.DLY.R.SW....GQASLTDGV.I..SFA..GS.FYSS.Y...VK..QK.SS.DYS.FD
Retrocopy EDAFCVVGITMTDLYSRGSWDSSSGQASLTDGVQI<ISFATDGSNFYSS*YADKVKVLQKTSSIDYSIFD

Parental  NYYIPEVTSVLLLRSCKTLTHEIGHIFGLRHCQWLACLMQGSNHLEEADRRPLNLCPICLRKLQCAIGFN
          .YYIP..TS.LLL.SC..LT.EI.HI..L.HCQ...CLMQGS.HLEE....PLNL.PI.L.KL.CA.GFN
Retrocopy KYYIPAMTSILLLQSCRILTYEIEHILRLQHCQGPTCLMQGSSHLEEVNHHPLNLRPIHLCKLHCASGFN

Parental  IVER
          I...
Retrocopy ISQK

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	0.03 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_440 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_440 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,