RetrogeneDB ID: retro_dord_439

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_18806:13910..14903(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000003524
• Aliases: None
• Description: None

Sequence

>retro_dord_439
ATGGCCACGGTGAAGTCGGAGCTCCTGAAGCCGGTGGCCTCGGAGAAGCCGGCGGCGCACAACAAGGTGTCGGTGATCGG
CACGGGGTCGGTGGGCATGGCGTGCGCCGTCAGCCTGCTGCTGAAGGGGCTGAGCGACGAGCTGGCGCTGGTGGACGTGA
ACGAGGACCTCCTGCGCGGCGAGACGATGGACCTGCAGCACGGCAGCACGTTCCTGAAGATGCCCGCCGTGGTGTGCAGC
ACGGACCTGGGCGTCACCGCCAACTCCAGCCTGGTGATCGTCACGGCCGGCGCGCGCCAGGCCAAGGGCGAGTCGCGCCT
GAACCTGGTGCAGCGGAACGTGGCCATCCTCAAGTCGGTGATCCCCAGCGTGGTGCAGCACAGCCCGCGCTGCAAGATGA
TCGTGGTCACCAACCCGGTGGACGTGCTGACCTACGTGGCCTGGAAGTTGAGCGCCCTGCCCCCGGCCCACATCATCGGC
AGCGGCTGCAACCTGGACACGGCGCGCTTCCGCTTCTTCATCGGGCAGAAGCTGGGCATCCACTCGGAGAGCTGCCACGG
CTGGGTCCTGGGCGAGCACGGCGACTCGAGCGTGCCCGTGTGGAGCGGCGTCAACGTGGCGGGCGTCCCGCTGCGGGAGC
TGAACCCGGGCCTCGGCGGCGACCAGGACCCCGAGCACTGGGAGAAGATCCACAAGGACGTGATCGCCAGCGCCTACCAG
ATCATCAAGATGAAGGGCTACACCAACTGGGCCATCGGCTTCTCGGTGGCCGACATCACGGAGAGCATCCTGCGCAACCT
GCGGAGGACGCACCCCGTGTCCACCGTGGCCAAGGGCCTCTACGGGATCCAGGAGGAGGTGTTCCTGAGCGTGCCGTGCG
TGCTGGGCGCGAACGGCATCGCCGACCTGGTCCGCGTCAAGCTCTCGCGCGACGAGGAGGCCCGAATGAAGAAGAGCGCC
GAGACGCTGTGGGCCATTCAGAAGGAGCTCAAG

Alignment

ORF - retro_dord_439 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.26 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGLKDQLIVNLLKEEYVLQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHGSL
          M...K..L......E.....NK..V.G.G.VGMACA.S.L.K.L.DELALVDV.ED.L.GE.MDLQHGS.
Retrocopy MATVKSELLKPVASEKPAAHNKVSVIGTGSVGMACAVSLLLKGLSDELALVDVNEDLLRGETMDLQHGST

Parental  FLKTPKIVSGKDYGVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKYSPNCKLLVVSNPV
          FLK.P..V...D.GVTANS.LVI.TAGARQ..GESRLNLVQRNV.I.K..IP.VV..SP.CK..VV.NPV
Retrocopy FLKMPAVVCSTDLGVTANSSLVIVTAGARQAKGESRLNLVQRNVAILKSVIPSVVQHSPRCKMIVVTNPV

Parental  DILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWILGEHGDSSVPVWSGVNVAGVS
          D.LTYVAWK.S..P....IGSGCNLD.ARFR...G..LG.H..SCHGW.LGEHGDSSVPVWSGVNVAGV.
Retrocopy DVLTYVAWKLSALPPAHIIGSGCNLDTARFRFFIGQKLGIHSESCHGWVLGEHGDSSVPVWSGVNVAGVP

Parental  FKNLNPDLGTDADKEQWKTVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGL
          ...LNP.LG.D.D.E.W...HK.V..SAY..IK.KGYT.WAIG.SVAD..ESI..NLRR.HP.ST..KGL
Retrocopy LRELNPGLGGDQDPEHWEKIHKDVIASAYQIIKMKGYTNWAIGFSVADITESILRNLRRTHPVSTVAKGL

Parental  YGIKDDVFLSVPCILGQNGISDVVKVTLTSEEEARLKKSADTLWGIQKELQ
          YGI...VFLSVPC.LG.NGI.D.V.V.L...EEAR.KKSA.TLW.IQKEL.
Retrocopy YGIQEEVFLSVPCVLGANGIADLVRVKLSRDEEARMKKSAETLWAIQKELK

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_439 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 7 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439 , retro_dord_449,
Felis catus	ENSFCAG00000015735	4 retrocopies	retro_fcat_102, retro_fcat_1839, retro_fcat_1919, retro_fcat_295,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Mustela putorius furo	ENSMPUG00000013730	5 retrocopies	retro_mputfur_1256, retro_mputfur_133, retro_mputfur_1446, retro_mputfur_1476, retro_mputfur_1565,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,