RetrogeneDB ID: retro_ecab_124

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:42515879..42516705(+)
• Located in intron of: ENSECAG00000014017

Retrocopy information

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

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_124
ATGCCTTTGCTCCTGGAGTGGCCCATGCTTTCCAGTACAACAGCCAGGGTACTGTGCCAGCACATCATGATGGAGTGGGA
GTTGCATGCAGCAACAGGAAGAAGAGCTGGACAAGGTGATGAAGGAAGAGCAGGAGACAAGGATGAAAAAGGACATGGAA
GAGAGAATGTCACCAGAGGAGATCAAGGAACAGATCCTGAAGGTGCAGGAGAAGCTTTTGGCCCTACAGGAAGAGAAGAA
TCTGCTTTTTCTGTAGCTCAAGAAAGTTTCACATGAGGAAGGGAAATGGAGGCGAAAGGAGCAGAGTGAGCTAACTACTC
TGGCATCTGATGCCTGCCCTTGGTGCCTCACTGTTCACACAGGAACTCGCCTCCTCAGCACACATAGCAGCCCTGGAGGA
CACAGTCCCCCAGGCATCCTCATGGCGACTGACAGAACCTAGCAGATGTTCGGACAGCAAGTGATTACAACCTGGCACTA
CAAGGGCGCAGCAGTTGCCTTTGCAGGGAGCCCAGAGCATGGGCGATTCCCAGAAAGCCCAGGTGGCACCTATGGGACTG
CTTAGCCCCCAACTCTCTATAGGCCCAGCCAGCCAGCCTATGGTCCCATGCAGCAGCTCAGAGCACCTTCAGCATTTCCT
GCAGTGTGATTCCTGTTTCAGCCGCAGCCTTAGGCAGTGCACAATGACTTTCAGGCCAGCCAGACAGGGTTTCTCCAGCC
TGGTGGTGTCCTGTCCTTACAAAAGCAGATGGAACACACCAAACAGCAGACCAGCTTCTCTGACTCATCCTCCCCGTGCC
CCATTCACCCCCAAGCTCTGCATCCC

Alignment

ORF - retro_ecab_124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 94.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPALLERPKLSNAMARALHRHIMMERERK-RQEEEEVDKMMEQKMKEEQERRKKKEMEERMSLEETKEQI
          MP.LLE.P.LS...AR.L..HIMME.E....Q.EEE.DK.....MKEEQE.R.KK.MEERMS.EE.KEQI
Retrocopy MPLLLEWPMLSSTTARVLCQHIMMEWELH>QQQEEELDKV----MKEEQETRMKKDMEERMSPEEIKEQI

Parental  LKLQEKLLALQEEKHQLFLQLKKVLHEEEKRRRKEQSDLTTLTSAAYQQGLTVHTGTHLLSMQGSPGGHN
          LK.QEKLLALQEEK..LFL.LKKV.HEE.K.RRKEQS.LTTL.S.A....LTVHTGT.LLS...SPGGH.
Retrocopy LKVQEKLLALQEEKNLLFL*LKKVSHEEGKWRRKEQSELTTLASDACPWCLTVHTGTRLLSTHSSPGGHS

Parental  RPGTLMAADRAKQMFGPQVLTTRHYVGSAAAFAGTPEHGQFQGSPGGAYGTAQPPPHYGPTQPAYSPSQQ
          .PG.LMA.DR..QMFG.QV.TT.HY.G.A.AFAG.PEHG.F..SPGG.YGTA.PP..Y.P.QPAY.P.QQ
Retrocopy PPGILMATDRT*QMFGQQVITTWHYKGAAVAFAGSPEHGRFPESPGGTYGTA*PPTLYRPSQPAYGPMQQ

Parental  LRAPSAFPAVQYLSQPQPQPYAVHSHFQPTQTGFLQPGGALSLQKQMEHANQQTGFSDSSSLRPMHPQAL
          LRAPSAFPAV..L...QPQP.AVH..FQ..QTGFLQPGG.LSLQKQMEH..QQT.FSDSSS..P.HPQAL
Retrocopy LRAPSAFPAV*FLF--QPQP*AVHNDFQASQTGFLQPGGVLSLQKQMEHTKQQTSFSDSSSPCPIHPQAL

Parental  HP
          HP
Retrocopy HP

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	0.05 RPM	14.40 RPM
SRP021940_placental_villous	0.05 RPM	9.81 RPM
SRP021940_synovial_membrane	0.05 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_124 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_124 has 0 orthologous retrocopies within eutheria group .

---

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,