RetrogeneDB ID: retro_ecab_889

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:74240950..74241941(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000015217
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CYTH2
• Ensembl ID: ENSECAG00000009878
• Aliases: None
• Description: cytohesin 2 [Source:HGNC Symbol;Acc:9502]

Sequence

>retro_ecab_889
AAGAACTTCAACATGGACCCCAAGAAGGGGATCCACTTCTTGCTGGATAATGAACTTCTCCAGAAGATACCCAACGAGCT
TGCCCCTTTCCTTTACAACGGCAAGGGCCTGAACAAGACAGCCTTGGGGATTACGTAGGGGAGAGGGAAGAGCTGAACCT
GGCAATGCTCCACGATTTTGTGAATCTGCGTGAGTTTACCGACCTCAATTTGGTGCAGGCCCTCAGGCAATTTCTATGGA
GCTTCCCGCCTCCCTGGAGAGGCCCAGGAGATTGACTGGATGATAGAAGCCTTCGCCCAGCCATACTGTCTGTGCAGCCC
TGGGGTTTTCCAGTCCACAAGCATGTCCTACGTGCTGTCTTTCACCATGATCATGCTGAGCACCACCAGCCTTTACAATC
CCAACGTCTGGGACAAGCTGGGCCTGGAGCACTTTGTGGCCATGAACCAGGGCAATCAACAAGGGCAGGACCAGCTTGAG
GAGCTGCTCAGGAACCTCTAGGACAGAACCTGAAATGAGCCCTTCCAGATTCCTGAGGATGATGGAAATGATCCGACCCA
CAGCTTCTTTAACCCAGACCGGGAAGGCTGGCTCCTTAAGCTGGGAGGGCTCTGCGTGAAGACATGGAAGCTGCTCTGGG
TTATCCTTACCCACAACTGCCTCTACTATTTTGAGTGCATGATGGACAAGGAGCCAGAGGAATCATACTCCTGGAGAATC
TGAGCAGCCTAGAGCTGGATGACCCCCAGAAACCTTCCTGCTTTGAGCTTTACATTCCCCAAAACGAGGGATAGCTCATC
AAAGCCAGGAAAATGGAGGCAGATGGCTGGGTGGTTGAGGAGAACCACATGGTGTACAGGTCTCAGCCCCATAGGAGGAG
AAGGACAAATGGAGCAAGTCCATCCAGGCAGCAGTGACTGTGGACCCCATCTATGAGATGCTGGTGGCAAGGGAGAAGGG
GATTTCTGTCAAGAAGCAGCAGGAACAGCCC

Alignment

ORF - retro_ecab_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.4 %
• Parental protein coverage: 83.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKFNMDPKKGIQFLVENELLQNTPEEIARFLYKGEGLNKTAIG-DYLGEREVLNLAVLHAFVNLHEFTVS
          K.FNMDPKKGI.FL..NELLQ..P.E.A.FLY.G.GLNKTA.G.DY.GERE.LNLA.LH.FVNL.EFT..
Retrocopy KNFNMDPKKGIHFLLDNELLQKIPNELAPFLYNGKGLNKTALG<DYVGEREELNLAMLHDFVNLREFTDL

Parental  NLVQALRQFLWSF-RLPGEAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSFAVIMLNT-SLHNPNVRD
          NLVQALRQFLWSF.RLPGEAQ.ID.M.EAFAQ.YCLC.PGVFQST...YVLSF..IML.T.SL.NPNV.D
Retrocopy NLVQALRQFLWSF>RLPGEAQEIDWMIEAFAQPYCLCSPGVFQSTSMSYVLSFTMIMLSTTSLYNPNVWD

Parental  KPGLERFVAMNRGINEGGDLPEELLRNLYDSIRNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGR-VKT
          K.GLE.FVAMN.G...G.D..EELLRNL.D...NEPF.IPEDDGND.TH.FFNPDREGWLLKLGG..VKT
Retrocopy KLGLEHFVAMNQGNQQGQDQLEELLRNL*DRT*NEPFQIPEDDGNDPTHSFFNPDREGWLLKLGGLCVKT

Parental  WKRRWFILTDNCLYYFEYTTDKEP-RGIIPLENLSIREVDDPRKPNCFELYIPNNKGQLIKACKTEADGR
          WK..W.ILT.NCLYYFE...DKEP.RGII.LENLS..E.DDP.KP.CFELYIP.N.G.LIKA.K.EADG.
Retrocopy WKLLWVILTHNCLYYFECMMDKEP<RGIILLENLSSLELDDPQKPSCFELYIPQNEG*LIKARKMEADGW

Parental  VVEGNHMVYR-ISAPTQEEKDEWIKSIQAAVSVDPFYEMLAARKKRISVKKKQEQP
          VVE.NHMVYR..SAP..EEKD.W.KSIQAAV.VDP.YEML.AR.K.ISVKK.QEQP
Retrocopy VVEENHMVYR<VSAP-*EEKDKWSKSIQAAVTVDPIYEMLVAREKGISVKKQQEQP

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	14.40 RPM
SRP021940_cerebellum	0.00 RPM	68.24 RPM
SRP021940_embryo	0.66 RPM	62.58 RPM
SRP021940_placental_villous	0.67 RPM	46.28 RPM
SRP021940_synovial_membrane	0.47 RPM	32.64 RPM
SRP021940_testis	2.62 RPM	68.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_889 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009878	1 retrocopy	retro_ecab_889 ,