RetrogeneDB ID: retro_ecab_1079

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:69842614..69843400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GLB2
• Ensembl ID: ENSECAG00000004437
• Aliases: None
• Description: SH3-domain GRB2-like endophilin B2 [Source:HGNC Symbol;Acc:10834]

Sequence

>retro_ecab_1079
GTGCCACTGTGGCCCAACCCCAGTGCCCGAGTGGAGGAGTTTCCATATGAGAAGCTAGACAGGAAGCTGACTTTGTGGGT
CACCAATATGGAACTGCTGCATCAGTCCATGTCAGAGATGGCCAGTGGGCTGGGCCCCACTGCTACCTAGGGGAAGACAT
TGATCAAGGTGGCAGAAACTGAAAAGTGCCTGGGAGATACAGAAGATTTTATCCTCATAGCCCCCACCAACTTCCTCATG
TCCCAGTGCAACTTCCAAGAAGGGGGCTGGAAGATGATTTCCAAGGAGGGGTGGCTCCTCCAAAACCTGTGTCTGGACTT
GAATGCCTGCAAAGCACTCCTGAAGAAGGCCAAGGCTGCAGAAGCCAAAGCCACAATGGTGCTTGAATTTCAGGAGACTT
GACCTTGTAATTAAATTCTCTCCAGCAGCGCCTCCCTGCTTTGGAATGATGAGGTGGACAAGACTGAGCAGGAGCTCCAA
GTAGCCCCAAAGGAGGTCGACCAGCAGGCAGAAGTGACCAGTCTCCTGCTGGAGGGAATCAGCTGCATTCACATGAAGCA
TCTTCGTTGCCTCTGTGAGTTCCTAGAGTCTCAGACAACTTATTACGTGCAGTGCTACTGCTGCATGCTGGACTTACATA
AACAGCTGGACAGATTTCCAGGCACCTTCATGGGTACAACAGAACCCACCTACCTGCCCCTGAGCAGCAAGTCACCCACC
ACCACAGCTACTGTGCCTGTGGTACCCTCTGTGGCTGGCCTGGCCTCTTTGGGGGAACCTGCTCTG

Alignment

ORF - retro_ecab_1079 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.21 %
• Parental protein coverage: 70.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLLQPNPSARVEEFLYEKLDRKVPSRVTNGELLAQYMAEAASELGPTTPYGKTLVKVAEAEKRLGAAERD
          V.L.PNPSARVEEF.YEKLDRK....VTN.ELL.Q.M.E.AS.LGPT...GKTL.KVAE.EK.LG..E.D
Retrocopy VPLWPNPSARVEEFPYEKLDRKLTLWVTNMELLHQSMSEMASGLGPTAT*GKTLIKVAETEKCLGDTE-D

Parental  FIHTASINFLTPLRNFLEGDWKTISKERRLLQNRRLDLDACKARLKKAKAAEAKATTVPDFQETRPRNYI
          FI..A..NFL....NF.EG.WK.ISKE..LLQN..LDL.ACKA.LKKAKAAEAKAT.V..FQET.P.N.I
Retrocopy FILIAPTNFLMSQCNFQEGGWKMISKEGWLLQNLCLDLNACKALLKKAKAAEAKATMVLEFQET*PCN*I

Parental  LSASASALWNDEVDKAEQELRVAQTEFDRQAEVTRLLLEGISSTHVNHLRCLHEFVESQTTYYAQCYRHM
          LS.SAS.LWNDEVDK.EQEL.VA..E.D.QAEVT.LLLEGIS..H..HLRCL.EF.ESQTTYY.QCY..M
Retrocopy LSSSASLLWNDEVDKTEQELQVAPKEVDQQAEVTSLLLEGISCIHMKHLRCLCEFLESQTTYYVQCYCCM

Parental  LDLQKQLGRFPGTFVGTTEPTSPPLSSTSPTTTAATMPVGPSVAGLGPPGEAAL
          LDL.KQL.RFPGTF.GTTEPT..PLSS.SPTTT.AT.PV.PSVAGL...GE.AL
Retrocopy LDLHKQLDRFPGTFMGTTEPTYLPLSSKSPTTT-ATVPVVPSVAGLASLGEPAL

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	254.99 RPM
SRP021940_embryo	0.00 RPM	48.56 RPM
SRP021940_placental_villous	0.00 RPM	78.04 RPM
SRP021940_synovial_membrane	0.00 RPM	32.04 RPM
SRP021940_testis	0.00 RPM	11.25 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1079 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1079 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1079 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
Callithrix jacchus	ENSCJAG00000020282	1 retrocopy	retro_cjac_2198,
Equus caballus	ENSECAG00000004437	1 retrocopy	retro_ecab_1079 ,