RetrogeneDB ID: retro_ecab_320

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 14:80441767..80442501(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000015302
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DGAT2
• Ensembl ID: ENSECAG00000024847
• Aliases: None
• Description: diacylglycerol O-acyltransferase 2 [Source:HGNC Symbol;Acc:16940]

Sequence

>retro_ecab_320
GAGCTGGTGAAGACGCACAACCTGCTCACCACCAGGAACTACATCTTTGGGTACCACCCCACGGCATCATGGGCCTCAGT
GCCTTCTGCTACTTCAGCACAGAGGCCACGGAAGTGAGCAAGAAGTTCCCTGGCATACGGCCCCACCTGGCCACGCTGGC
CGGCAGCTTCCGGAGGCCAGTGCTGAGGGAGTACATGGTGTCTGGAGGCATCTGCCCTGTGAACCAGGACACAGTAGACT
TGCTTTCAAAGAATGGGAGTGGCAATGCCATCATCCTCGTTGTGGGGGGCGCGGCCGAGTCCCTGAGCTCCATGCCCGGC
AAGAACGCGGTCACCCTGCGCCACCGCAAGGGCTTAGTGAAACTGGCTCTGCGCCATGGAGCCGATCTGGTTCCTTTCTA
CTCCTTCGGGGAGAACGAGGTGTACAAGCAGGTAATCTTTGAGGAGGGCTCCTGGGGCCGCTGGGTCCAGAAGAAGTTCC
AGAGGTACATCGGCTTCGCCCGGTGCATTTTCCATGGCCGAGGCCTCTTCTCCTCTGACACCTGGGGGCTCCTGCCCTAC
CCGAAGCCCATCACCTCCGTCGTGGGTGAGCCCATCACCATCCCCAAGCTGGAGCACCCAACCCAGCAGGACATCGACCT
GTACCACACCATGTACATGGAGGCCCTGGTGAACCCCTTCTACAGGCACAAGACCAAGTCTGGCCTCCCGGGGACTGAGG
TCCTGGAGTGAACT

Alignment

ORF - retro_ecab_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.69 %
• Parental protein coverage: 80.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLVKTHNLLTTRNYIFGYHP-HGIMGLGAFCNFSTEATEVSKKFPGIRPYLATLAGNFRMPVLREYLMSG
          .LVKTHNLLTTRNYIFGYHP.HGIMGL.AFC.FSTEATEVSKKFPGIRP.LATLAG.FR.PVLREY..SG
Retrocopy ELVKTHNLLTTRNYIFGYHP<HGIMGLSAFCYFSTEATEVSKKFPGIRPHLATLAGSFRRPVLREYMVSG

Parental  GICPVNQDTIDYLLSKNGSGNAIIIVVGGAAESLSSMPGKNAVTLRHRKGFVKLALRHGADLVPIYSFGE
          GICPVNQDT.D.LLSKNGSGNAII.VVGGAAESLSSMPGKNAVTLRHRKG.VKLALRHGADLVP.YSFGE
Retrocopy GICPVNQDTVD-LLSKNGSGNAIILVVGGAAESLSSMPGKNAVTLRHRKGLVKLALRHGADLVPFYSFGE

Parental  NEVYKQVIFEEGSWGRWVQKKFQKYIGFAPCIFHGRGLFSSDTWGLLPYPKPITTVVGEPITIPKLEHPT
          NEVYKQVIFEEGSWGRWVQKKFQ.YIGFA.CIFHGRGLFSSDTWGLLPYPKPIT.VVGEPITIPKLEHPT
Retrocopy NEVYKQVIFEEGSWGRWVQKKFQRYIGFARCIFHGRGLFSSDTWGLLPYPKPITSVVGEPITIPKLEHPT

Parental  QQDIDLYHAMYMEALVNLFDRHKTKFGLPETEVLEVT
          QQDIDLYH.MYMEALVN.F.RHKTK.GLP.TEVLE.T
Retrocopy QQDIDLYHTMYMEALVNPFYRHKTKSGLPGTEVLE*T

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	1.59 RPM
SRP021940_cerebellum	0.16 RPM	13.04 RPM
SRP021940_embryo	0.00 RPM	7.88 RPM
SRP021940_placental_villous	0.00 RPM	0.67 RPM
SRP021940_synovial_membrane	0.00 RPM	2.00 RPM
SRP021940_testis	0.13 RPM	112.16 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_320 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_320 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_320 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000024847	1 retrocopy	retro_ecab_320 ,
Myotis lucifugus	ENSMLUG00000017447	1 retrocopy	retro_mluc_1157,