RetrogeneDB ID: retro_ecab_480

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:4283869..4284363(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003844
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSECAG00000010635
• Aliases: None
• Description: G protein pathway suppressor 2 [Source:HGNC Symbol;Acc:4550]

Sequence

>retro_ecab_480
TCAGCACGCGGGAGCCCTGGAGGATGCCATAGCCCAGTGCCCTCACGGCAGCCGACAGAGCCAAACAGATGTTTGGACCC
AAGTGCTTCCAACCCAGCACTATATGGGCTCAGCAGCTGCTTTCGAGAGACCGCAGAACACGGGCAATACCAAGACAGCC
CAGGCACGCCCATGGACTGCTCAGCCCCAGCTCACCACACACCCGCCCAGCCAGCCCATAGTCCTGGTCAGCAGCTCAGA
GCACACGTAAGTGCTTCCTGCAGCACGGTGCCCATCTCAGCCTCAGTCGCAGCCACCGCCCCGTGCTGTGCATGGCCACT
TTCAGCCCACCAGACAGGGCTCCTGCAGCCTGCCGGGGCCCCATCCTTGCAGAAGCAGATGGATGTGCCAACCAGTGGAC
TGGCTTCTCTGACTTATCCTCCCTGTGCCCCACACACCCCAGCTCTGCATCCAGCCCCTGGGTTCCTTCCGACCCCTAGC
CCCCTGTGCAGATG

Alignment

ORF - retro_ecab_480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.58 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  SMQGSPGGHNRP-GTLMAADRAKQMFGP-QVLTTRHYVGSAAAFAG-TPEHGQFQGSPGG-AYG-TAQP-
          S..GSPGG...P...L.AADRAKQMFGP.QVL.T.HY.GSAAAF...T.EHGQ.Q.SPG..A.G.TAQP.
Retrocopy SARGSPGGCHSP<SALTAADRAKQMFGP<QVLPTQHYMGSAAAFER<TAEHGQYQDSPGT<AHG<TAQP<

Parental  PPHYGPTQPAYSPSQQLRAPSA-FPAVQYLSQPQ--PQPYAVHSHFQPT-QTGFLQPGGALSLQKQME-H
          P.H..P.QPA.SP.QQLRA.....PA....SQPQ..P.P.AVH.HFQPT.QTG.LQP.GA.SLQKQM...
Retrocopy PAHHTPAQPAHSPGQQLRAHVS>LPAARCPSQPQSQPPPRAVHGHFQPT<QTGLLQPAGAPSLQKQMD<C

Parental  ANQQTGFSDSSSLRPMHPQALHPAPGLLASPQLPVQM
          ANQ.TGFSD.SSL.P.HP......P.....P..PVQM
Retrocopy ANQWTGFSDLSSLCPTHPSSA-SSPWVPSDP*PPVQM

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	12.57 RPM
SRP021940_cerebellum	0.00 RPM	12.36 RPM
SRP021940_embryo	0.00 RPM	14.40 RPM
SRP021940_placental_villous	0.00 RPM	9.81 RPM
SRP021940_synovial_membrane	0.00 RPM	12.77 RPM
SRP021940_testis	0.00 RPM	53.20 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_480 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_480 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_480 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480 ,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,