RetrogeneDB ID: retro_dord_714

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_6017:16297..17605(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Smek1
• Ensembl ID: ENSDORG00000012467
• Aliases: None
• Description: SMEK homolog 1, suppressor of mek1 (Dictyostelium) [Source:MGI Symbol;Acc:MGI:1915984]

Sequence

>retro_dord_714
TCGCTAATTCTACAGTCCAAGATACGTGGGACTACAAATTATCAGAAGCAAAAGGGACTGCTAATTATCTGGTCTGAATC
TGAAGACCATGGTACGGCGCTAAGCTTTCAAGACCCGAAATGTTGTACAGATATCTGGGAGGATATCTGCTTAGTTCAAG
GTAAAGATCCATCTCTGGAAAATACACAGGGGTTTTGGGATGATTCAGTAAACAACCATGGAATGCCACCAATCAGTTAT
CTCCCTGAGCTTCCAACCTGTGAAGTTGCTACCTTGGGTCAAATTGCAGATTTAATTGGTTCTGTTTCCACCTCAAATAT
CCAAAGGGAAAGACTGGCTCTAATCTTGGAAAGTGAAGATTATATTAAACAACTAATGAAGATCTTTCATACTTGTGAGA
ATCTTCAGAATACCGAATGCTTACACCATTTATATAACATTATTAAAGGCATCTTATTCTTTAATAAGACTTCACTATTT
GACATCATGCTGTCTGATACATATATTATGGATGTTATAGGGTGCCTGGAATATGATCCCTGTTTGCCTGAGCCAAAAAG
GCATAGGGAATTCTTAACCAAAAGTGCGAAGTTTAAGGAAGTTATACCAATTACAGACTCTGAACTAAGACACAAAATAC
ACCAGACATACCTAGTGCAATATATTCATGACATTCTTCTGCCTGTGCCATCAATCTTTGATGAAAACCATCTTTCCACC
TTTACAACATTTATTTTTGCCAGAAAGGTTGACATAGTTAACATGCTACAAGAAGACAAAAAGGTCTTATTTGAAGTTTT
TGCACAGTTAAAGGATAAGACAACAGATGATGAAAAACGCCGTGAACTGTTACTTTTCTTCAAGGAATTCTGTGAATTTT
CCCAAGCATTACAGAATCAAAACAAGATTGCACTATTCCAAACATTGATACAACTTGGAATCATACCTGCTCTTAAAATT
GTAATTAACATGAAGGATTTTCAAATGAAGTCAATGGCTACAGATATACTTACTTATCTAGTGGACTATAATCCATTCAT
GGTCCAAAAATGTGTCATGGAGGAAGTTGAAGAAGGAGAAGAGAACGAACTCACCGTTAATATACTAATTCAACAAATGA
TTCATGATACTGATCCTGAGCTTGGAAATGCGATTAATTTGATGGTACTTCTTCGTTCTTTACTCAACCCAGTGAACATG
CTAGTAACGCCTGATGAATGTGAAAGAATTGAATTTCTGAATTTCTTCTATAGATATTGCATGCATAATTTGATAGCACC
ACTTTTATGCACCACTTCAGAAGACAAA

Alignment

ORF - retro_dord_714 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.11 %
• Parental protein coverage: 56.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLLLESKINPNTAYQKQQDTLIVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVDITQDLVDESE
          SL.L.SKI...T.YQKQ...LI.WSE.E....ALSFQ....C..IWE.IC.VQGKDPS...TQ...D.S.
Retrocopy SLILQSKIRGTTNYQKQKGLLIIWSESEDHGTALSFQDPKCCTDIWEDICLVQGKDPSLENTQGFWDDSV

Parental  EERFDDMSSPGLELPSCELSRLEEIAELVASSLPSPLRREKLALALENEGYIKKLLELFHVCEDLENIEG
          ........S...ELP.CE...L..IA.L..S...S...RE.LAL.LE.E.YIK.L...FH.CE.L.N.E.
Retrocopy NNHGMPPISYLPELPTCEVATLGQIADLIGSVSTSNIQRERLALILESEDYIKQLMKIFHTCENLQNTEC

Parental  LHHLYEIIKGIFLLNRTALFEVMFSEECIMDVIGCLEYDPALSQPRKHREFLTKTAKFKEVIPISDPELK
          LHHLY.IIKGI...N.T.LF..M.S...IMDVIGCLEYDP.L..P..HREFLTK.AKFKEVIPI.D.EL.
Retrocopy LHHLYNIIKGILFFNKTSLFDIMLSDTYIMDVIGCLEYDPCLPEPKRHREFLTKSAKFKEVIPITDSELR

Parental  QKIHQTYRVQYIQDMVLPTPSVFEENMLSTLHSFIFFNKVEIVGMLQEDEKFLTDLFAQLTDEATDEEKR
          .KIHQTY.VQYI.D..LP.PS.F.EN.LST...FIF..KV.IV.MLQED.K.L...FAQL.D..TD.EKR
Retrocopy HKIHQTYLVQYIHDILLPVPSIFDENHLSTFTTFIFARKVDIVNMLQEDKKVLFEVFAQLKDKTTDDEKR

Parental  QELVNFLKEFCAFSQTLQPQNRDAFFKTLSNMGILPALEVILGMDDTQVRSAATDIFSYLVEYNPSMVRE
          .EL..F.KEFC.FSQ.LQ.QN..A.F.TL...GI.PAL.....M.D.Q..S.ATDI..YLV.YNP.MV..
Retrocopy RELLLFFKEFCEFSQALQNQNKIALFQTLIQLGIIPALKIVINMKDFQMKSMATDILTYLVDYNPFMVQK

Parental  FVMQEAQQNDDDILLINLIIEHMICDTDPELGGAVQLMGLLRTLVDPENMLATANKTEKTEFLGFFYKHC
          .VM.E........L..N..I..MI.DTDPELG.A..LM.LLR.L..P.NML.T....E..EFL.FFY..C
Retrocopy CVMEEVEEGEENELTVNILIQQMIHDTDPELGNAINLMVLLRSLLNPVNMLVTPDECERIEFLNFFYRYC

Parental  MHVLTAPLLANTTEDK
          MH.L.APLL..T.EDK
Retrocopy MHNLIAPLLCTTSEDK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq

Dipodomys ordii was not studied using ChIP-Seq data.

EST

Dipodomys ordii was not studied using EST data.

TSS

Dipodomys ordii was not studied using FANTOM5 data.

Lab

retro_dord_714 was not experimentally validated.

Homology

Retrocopy orthology:

Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012467	1 retrocopy	retro_dord_714 ,
Erinaceus europaeus	ENSEEUG00000006324	1 retrocopy	retro_eeur_316,
Pan troglodytes	ENSPTRG00000006638	1 retrocopy	retro_ptro_124,
Pteropus vampyrus	ENSPVAG00000015294	1 retrocopy	retro_pvam_1091,
Tupaia belangeri	ENSTBEG00000008535	1 retrocopy	retro_tbel_2368,
Tarsius syrichta	ENSTSYG00000010333	1 retrocopy	retro_tsyr_863,
Tursiops truncatus	ENSTTRG00000013598	1 retrocopy	retro_ttru_1398,
Vicugna pacos	ENSVPAG00000002765	1 retrocopy	retro_vpac_536,