RetrogeneDB ID: retro_ecab_330

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:48805092..48806178(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSECAG00000018845
• Aliases: None
• Description: polypyrimidine tract binding protein 1 [Source:HGNC Symbol;Acc:9583]

Sequence

>retro_ecab_330
TTCTACCCGGTGACCCTGGACGTGCTCCACCAGATCTTCTCCAAGTTCGGCACGGTGCTGAAGATCATCACCTTCACCAG
GAACAACCAGTTCCAGGCGCTGCTGCAGTACGCGGAGGCTGTGAGCGCGCAGCACGCCAAGCTGTCGCTGGACGGCCAGA
ACGTCTACAACGCCTGCTCCACGCTGCGCATCGACTTCTCCAAGCTCACCAGCCTCAACGTCAAGCACAAGAGCGGCGAC
TACGCGCGCCCCGACCTGCCCTCGGGCGACAGCCAGCCTTCGCTGAACCAGACCATGGCCGAGCCTTTCGTTGCGCTTGG
TATAATGTCAGCCTCTCCATATGCAGGAGCTGGTTTCTCTCCCACCTTTGCCAGTCCTCAAGCCGCAGGCCTCTCTGTTT
CCCAACGTGCACGGGGCATTGGCCCCCCGGCCATTCCCGTCCGCGGCGCAGCGGCAGCAGCGGGCAGGATCGCCTCTCCC
GGACCTGGCTGGGCCGGGAACTCCGTGCTGCTGGTCAGCAACCTGAACCCCGAGAGAGTCACACCCCAAAGCCTCTTTAT
TCTTTTCAGCGTGTACGGTGACATGCAGCGGGTGAAGATCCTCTTCAACAAGAAGGAGAACGCGCTGGTGCAGATGGCCG
ACGGCAGCCAGGCCCAGCTGGCCATGAGCCACCTCAACGGGCACAAGCTGCACGGGAAGCCGGTGCGCATCACGGCGTCC
AAGCACCAGAACGTGCAGCTGCCCCGCGAGGGCCAGGAGGACCAGGGCCTCACCAAGGACTACGGTAGCTCGCCGCTGCA
CCGCTTCAAGAAACTGGGCTCCAAGAACTTCCAGAACATCTTCCCGCCCTCCGCCATCCTGCACCTCTCCAACATCCCGC
CATCCAAATCCGAGGACGACCTCAAGATCCTCTTCTCCAGCAACGGCGGGATTGTCAAGGGGTTCAAGTTCTTCCAGAAG
GACCAGAAGATGGCGTTGATCCAGATGGGCTCGGTGGAGGACGCGATCCTGGCGCTCATCAACCTGTACAACCACGACCT
GGGCGAGAACCACCACCTGCGGGTCTCCTTCTCCAAGTCCACCATC

Alignment

ORF - retro_ecab_330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.56 %
• Parental protein coverage: 65.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYAEPVSAQHAKLLLDAQNIYNARCTLRIDFSK-T
          FYPVTLDVLHQIFSKFGTVLKIITFT.NNQFQALLQYAE.VSAQHAKL.LD.QN.YNA..TLRIDFSK.T
Retrocopy FYPVTLDVLHQIFSKFGTVLKIITFTRNNQFQALLQYAEAVSAQHAKLSLDGQNVYNACSTLRIDFSKLT

Parental  SLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFGAPGIMSASPYAGAGFPPTFAIPQAAGLSV-PNV
          SLNVK....KS.DY.RPDLPSGDSQPSL.QTMA..F.A.GIMSASPYAGAGF.PTFA.PQAAGLSV.PNV
Retrocopy SLNVKH---KSGDYARPDLPSGDSQPSLNQTMAEPFVALGIMSASPYAGAGFSPTFASPQAAGLSV>PNV

Parental  HGALAPLAIPSAA-AAAAAGRIALPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK
          HGALAP...PSAA.AAAAAGRIA.PG...AGNSVLLVSNLNPERVTPQSLFILF.VYGD.QRVKILFNKK
Retrocopy HGALAPRPFPSAA<AAAAAGRIASPGPGWAGNSVLLVSNLNPERVTPQSLFILFSVYGDMQRVKILFNKK

Parental  ENALVQMADGSQAQLAMSHLNGHKLHGKPVRITLSKHQNVQLPREGQEDQGLTKDYGSSPLHRFKKPGSK
          ENALVQMADGSQAQLAMSHLNGHKLHGKPVRIT.SKHQNVQLPREGQEDQGLTKDYGSSPLHRFKK.GSK
Retrocopy ENALVQMADGSQAQLAMSHLNGHKLHGKPVRITASKHQNVQLPREGQEDQGLTKDYGSSPLHRFKKLGSK

Parental  NFQNIFPPSATLHLSNIPPSISEDDLKILFSSNGGIVMGFKFFQKDRKMALIQMGSVEEAIQALIDLHNH
          NFQNIFPPSA.LHLSNIPPS.SEDDLKILFSSNGGIV.GFKFFQKD.KMALIQMGSVE.AI.ALI.L.NH
Retrocopy NFQNIFPPSAILHLSNIPPSKSEDDLKILFSSNGGIVKGFKFFQKDQKMALIQMGSVEDAILALINLYNH

Parental  DLGENHHLRVSFSKSTI
          DLGENHHLRVSFSKSTI
Retrocopy DLGENHHLRVSFSKSTI

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	4.60 RPM	102.00 RPM
SRP021940_cerebellum	1.71 RPM	27.32 RPM
SRP021940_embryo	18.49 RPM	263.48 RPM
SRP021940_placental_villous	5.34 RPM	109.98 RPM
SRP021940_synovial_membrane	8.98 RPM	153.79 RPM
SRP021940_testis	5.88 RPM	80.89 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_330 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330 ,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,