RetrogeneDB ID: retro_dord_781

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_971:127930..129307(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snw1
• Ensembl ID: ENSDORG00000012380
• Aliases: None
• Description: SNW domain containing 1 [Source:MGI Symbol;Acc:MGI:1913604]

Sequence

>retro_dord_781
ATGGCACTGACCAACTTTTTACCCGCACCTACTCAGCTATCCCAGGACCAACTTGAAGCTGAAGAGAAGGCAAGATCTCA
CAGGTCCTGGCAGACCTGTCTGGCATCCTCACGCAGAGAAGCTCCCCCGTATGGGTGCCAAAAAGGTTGGAATCCTTGCT
CGCTAGAAGATTTTGGAGATGGAGGTGCTTTTCCAGAGATCCATGTGGCCCAGTATCCACTGGATATGGGACGACAACAA
ACCAGGTCAAATGCGCTGGCCATTCAGGTCGATCCTGAAGGAAGAATTCGGTACGATGCAGTTGCTCGACAAGGTCAGTC
AAAAGACAAGGTCATTTACAGCAAATATACTGACCTGGTGCCACAGGAGGGGATGAATGCCGGTGATCCAGACCCACAGA
GACCCAATGAAGAAGCTATTCAAGAGATCACAGCAAAGACAAGGGTAGCCTTAGAGAAGTGTGTGCAGCAGAAGGTTGCC
TCAGCCATGCCAGTTTGAGCAGCTGATCAATCGGCTCCTGCTCAGTATCTGCAATACACACCATCTCAGCAAGGAGTGGC
ATTGAACTCTGGAGCTACACAGATGCTCATTTGCATGGTAGAGATGCAGACAGATCCAATGGAGCCTCCGAGGTTCCGGA
TCAACCAGAAGATTCCCCGGGGACCACCTTCTCCTCCTGCACCTGTCATGCACTCTCCAAGCCAAAAGATGACTGCCAAG
GAGCAACAAGAGTGGAAGATTCCTCCTTGCATCTCCAACTGGAAAAATGCAAAGGGTTATACAATTCCTTTAGACAAGCG
ACTGGCCGCCGATGGAAGAGGATTTCAGATGGTACACATCAATGAGACCTTTGCCAAACTCACCGAAGCTCTCTACATTG
CCGATCAGAAGGCTCGGGAGGCTGTGGAAACACGGGCCCAAGTGGAGAGAAAAAGGGCCCAGAAAGCAAAAGAGAAGCAT
GAAAAGAAACTTAGAGTGATGGCCCAAAAAGCCAGGAAGAGGAGAGCTGGCATCAAAACCTGTGTGGACAGAGATGATGG
GGAGGCACGTGGGAGGGAGGAGATCCAGCATGAGAGGCAAAGAGAGACAGCATGACCGGAATCTGAGAAGAGATGGAAAC
CGCAGAGGAAGGAACATCGAGATATCACTGAAGTCATCACTGAAGTTCTTGGTGTCCCCAATCCTTGCACCTCAAATGTT
CAGTATAACCAAAGGCTCTTCAACCAGTCTAAGGGTATGGACAGTGGATTTTCAGGTAGAGAAGATGAAATTTACAATAT
TTATGATCACTCCTGGAGAAGTAGTAAAGCCATGGCCCATAGTGTCTATTATCCCAATGAGAATCTGCACAAGAACAAGT
CTAGTGATGACCTAGAG

Alignment

ORF - retro_dord_781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.72 %
• Parental protein coverage: 86.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
          MALT.FLPAPTQLSQDQLEAEEKARS.RS.QT.L.SSRRE.PPYG..KGW.P..LEDFGDGGAFPEIHVA
Retrocopy MALTNFLPAPTQLSQDQLEAEEKARSHRSWQTCLASSRREAPPYGCQKGWNPCSLEDFGDGGAFPEIHVA

Parental  QYPLDMGRKKKMSNALAIQVDPEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEAI
          QYPLDMGR....SNALAIQVDPEG.I.YDA.ARQGQSKDKVIYSKYTDLVP.E.MNA.DPD.QRP.EEAI
Retrocopy QYPLDMGRQQTRSNALAIQVDPEGRIRYDAVARQGQSKDKVIYSKYTDLVPQEGMNAGDPDPQRPNEEAI

Parental  KEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEPP
          .EIT.KTRVALEK.V.QKVA.AMPV.AAD..APAQY..YTPSQQGVA.NSGA.Q..I.MVEMQ.DPMEPP
Retrocopy QEITAKTRVALEKCVQQKVASAMPV*AADQSAPAQYLQYTPSQQGVALNSGATQMLICMVEMQTDPMEPP

Parental  RFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVHI
          RF.IN.KIPRGPPSPPAPVMHSPS.KMT.KEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRG.Q.VHI
Retrocopy RFRINQKIPRGPPSPPAPVMHSPSQKMTAKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGFQMVHI

Parental  NENFAKLAEALYIADRKAREAVETRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEAR
          NE.FAKL.EALYIAD.KAREAVETRAQVERK.AQK.KEKHE.KLR.MAQKAR.RRAGIKT.V...DGEAR
Retrocopy NETFAKLTEALYIADQKAREAVETRAQVERKRAQKAKEKHEKKLRVMAQKARKRRAGIKTCVDRDDGEAR

Parental  ERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMDS
          .R.EI.H.R..E........R..P....K..R.....I.EV..LGVPNP.TSN.VQY.QRLFNQSKGMDS
Retrocopy GREEIQHERQRETA*PESEKRWKPQR--KEHRDITEVITEV--LGVPNPCTSN-VQYNQRLFNQSKGMDS

Parental  GFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLE
          GF.G.EDEIYN.YD..WR..K.MA.S.Y.P..NL.K....DDLE
Retrocopy GFSGREDEIYNIYDHSWRSSKAMAHSVYYPNENLHKNKSSDDLE

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_781 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Callithrix jacchus	ENSCJAG00000016947	2 retrocopies	retro_cjac_2932, retro_cjac_576,
Dipodomys ordii	ENSDORG00000012380	3 retrocopies	retro_dord_693, retro_dord_781 , retro_dord_782,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Homo sapiens	ENSG00000100603	1 retrocopy	retro_hsap_174,
Gorilla gorilla	ENSGGOG00000026016	1 retrocopy	retro_ggor_257,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys	ENSNLEG00000016771	1 retrocopy	retro_nleu_982,
Ochotona princeps	ENSOPRG00000007568	1 retrocopy	retro_opri_737,
Pongo abelii	ENSPPYG00000006031	1 retrocopy	retro_pabe_454,
Pan troglodytes	ENSPTRG00000006587	1 retrocopy	retro_ptro_165,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,
Tarsius syrichta	ENSTSYG00000010951	1 retrocopy	retro_tsyr_1871,