RetrogeneDB ID: retro_ecab_668

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 27:621463..622180(+)
• 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_668
TCTCTGGACCAGGCATTGAAGGAAGCCAAGAGAATTCCCAAGAGATTCTGGGGAAGCTCCACATTGCAATTCCCTGAGGC
TTGGGGTATCCCCAAGAAAAGCACCCCAATCATGCACCAAGATGTGAAATCTTCTAACAGCCTCGTCAACTGCAGAGGGG
AGATCAAGCTGTGAAATTTTGGGGTGAATGGGCAGCTCGACTCCACAGCCAACCCCTTTGTAGGAACTCATTCCTACACA
TCTCTGAGCAGTTGCAAGACACTCACTGCTTGGTGCAGTCAGGCATCGGGAGCACGGCCTGTCCCTCAGAAGCTGTCCGT
GGGAAGGTACCCCATCCCTTTCCTGATGCCAAGGAGCTGAGGCCGTATCTGGCTGGGCCATGGTCGGGGGAGTGGAAGGA
GAGCCTCCTAGCATCTTCCGAAGACCAAGAGCACCTGGACACCCCACAGTGGCCACAGATGGATAGTTGGCCAGCTCTGG
CCGTCTTGGAACTGCCGGATGGTATTGTGAAGGAGCTTCTTTCCAAGCTGCCACCAGCACCTTCACTCAGGACCTCAAGG
AGTTTCAAATAAATGCCTAATTGAGAACCCAGCACATCTGAAGATGCTCATGAGCCAGGCTTTATCAAATGGTACAAATG
GTTGAAGTGTATTTGTCAGCTGGTTGTGTAAAATGCTGCCACTGAACCAGCCTGGCACACCCATGTGCACCTCCATG

Alignment

ORF - retro_ecab_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.08 %
• Parental protein coverage: 67.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

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

Parental  SMANSFVGTRSYMS-PERLQGTHYSVQSDIWSM-GLSL-VELSVGRYPI-PPPDAKEL-EAIFGRPVVDG
          S.AN.FVGT.SY.S..E.LQ.TH..VQS.I.S..GLSL...LSVGRYPI.P.PDAKEL.EA..G...V.G
Retrocopy STANPFVGTHSYTS<SEQLQDTHCLVQSGIGST<GLSL<QKLSVGRYPI<PFPDAKEL<EAVSGWAMVGG

Parental  AEDEPPSTSPRPRPPGRAI-SGH-GMDSRPAMAIFELLDYIVNEPPHKLP-HGAFTQDFQEF-VNKCLIK
          .E.EPPS...RPR.PG....SGH..MDS.PA.A..EL.D.IV.E...KLP....FTQD..EF..NKCLI.
Retrocopy VEGEPPSIFRRPRAPGHPT<SGH<QMDSWPALAVLELPDGIVKELLSKLP<TSTFTQDLKEF<SNKCLIE

Parental  NPAERADLKMLMNHAFIKRSEVEEVDFAGWLCKTLRLNQPSTPTRTAV
          NPA....LKMLM..A.........V.F..WLCK.L.LNQP.TP..T..
Retrocopy NPAH---LKMLMSQALSNGTNG*SV-FVSWLCKMLPLNQPGTPMCTSM

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	0.00 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_668 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_668 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,