RetrogeneDB ID: retro_ecab_968

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:30345592..30346161(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP2K2
• Ensembl ID: ENSECAG00000009157
• Aliases: None
• Description: mitogen-activated protein kinase kinase 2 [Source:HGNC Symbol;Acc:6842]

Sequence

>retro_ecab_968
TCTCTGGACCAGGCATTGAAGGAAGCCAAGAGAATTCCCAAGAGATTCTGGGGAAGCTCCACATTGCAATTCCCTGAGGC
TTGGGGTATCCCCAAGAAAAGCACACCAATCATGCACCAAGATGTGAAATCTTCTAACAGCCTCGTCAACTGCAGAGGGG
AGATCAAGCCGTGCAATTTTGGGGTGAACGGGCAGCTTGACTCCACAGCCAACCCCGTTGTAGGAACTCGATCCTACACA
TCTCTGAGCAGTTGCAAGACACTCACTGATCGGTGCAGTCAGGCATCGGGAGCACGGCCTGTCCCTGGAGAAGCTGTCCG
TGGGAAGGTACCCCATCCCTCTCCTGATGCCAAGGAGCTGAGGCAATATCTGGCTGGGCCATGGTCGGGGGGGGTGGAAG
GAGAGCCTCCTAGCATCTTCCCAAGGCAAAGAGCACCTGGACACCCCGCAGCGGCCACAGATGGATAGCTGGCCAGCTCT
GGCCATCTTGCAACTGCCGGATGGTATTGTGAAGGAGCTTGCTTTCCAAGCTGGCCACCAGCAGCTTCGCTCAGGACCTC
AAGGAGTTT

Alignment

ORF - retro_ecab_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.0 %
• Parental protein coverage: 52.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  SLDQVLKEAKRIP-EEILGKVSIAVLRGLAYLREKH-QIMHRDVKPSNILVNSRGEIKLCDFGVSGQLID
          SLDQ.LKEAKRIP..EILGK..IA...GL.Y..EKH..IMH.DVK.SN.LVN.RGEIK.C.FGV.GQL.D
Retrocopy SLDQALKEAKRIP<QEILGKLHIAIP*GLGYPQEKH>PIMHQDVKSSNSLVNCRGEIKPCNFGVNGQL-D

Parental  SMANSFVGTRSYMS-PERLQGTHYSVQSDIWSM-GLSLVELSVGRYPI-PPPDAKELEAIFGRPVVDGAE
          S.AN..VGTRSY.S..E.LQ.TH.SVQS.I.S..GLSL..LSVGRYPI.P.PDAKEL......P.....E
Retrocopy STANPVVGTRSYTS<SEQLQDTH*SVQSGIGST<GLSLEKLSVGRYPI<PSPDAKELRQYLAGPWXXXXE

Parental  DEPPSTSPRPRPPGRAI-SGH-GMDSRPAMAIFELLDYIVNEPP-HKLPHGAFTQDFQEF
          .EPPS..PR.R.PG....SGH..MDS.PA.AI..L.D.IV.E....KL....F.QD..EF
Retrocopy GEPPSIFPRQRAPGHPA<SGH<QMDSWPALAILQLPDGIVKELA>SKLATSSFAQDLKEF

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	24.03 RPM
SRP021940_cerebellum	0.00 RPM	47.88 RPM
SRP021940_embryo	0.03 RPM	51.43 RPM
SRP021940_placental_villous	0.00 RPM	25.31 RPM
SRP021940_synovial_membrane	0.00 RPM	44.53 RPM
SRP021940_testis	0.00 RPM	21.74 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_968 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_968 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015084	1 retrocopy	retro_cjac_4061,
Equus caballus	ENSECAG00000009157	2 retrocopies	retro_ecab_668, retro_ecab_968 ,
Homo sapiens	ENSG00000126934	1 retrocopy	retro_hsap_3785,
Gorilla gorilla	ENSGGOG00000008832	1 retrocopy	retro_ggor_115,
Nomascus leucogenys	ENSNLEG00000003013	1 retrocopy	retro_nleu_1121,
Otolemur garnettii	ENSOGAG00000001658	1 retrocopy	retro_ogar_576,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566,