RetrogeneDB ID: retro_dord_89

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_2627:128083..128824(-)
• Located in intron of: ENSDORG00000012792

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000007375
• Aliases: None
• Description: None

Sequence

>retro_dord_89
ATGGCAGATGACGCCATGCAGCGGGAGGGCCCGGAAGTCCCGTGGCCCAGGCTTGGGAGGCCGTGGCGGCTTCTGTGGAG
GCTTCAGTAGTGGCCTCTGGGTCGAGGCTGCGACTGTGGTAGAGGCCAGGGTCGTGGCCATGGGACTCGTGGAGGCAAGG
CTGAAGACAAGGAATGGATCCCCATCGCCAAACTGGGCTGCCTGGTTAAGGACATGAAGATCAAGTCTCTGGAGGAGATC
TATCTTTCCTCCCTGTCCATCAAGGAGTCTGAGATTGTTGACTTCTTCCTGGGGGGTCATCCAGGATGAGGGGTTGAAGA
TTATGCCCGGGCAGAAGCAGACTGGAGCTGGCCAGCGCACCAGGTTCAAGGCATTTGTAGCCATTGGCTACTACAACAGC
CACGTTGGTCTGGGGGTTCAGTGCGCCAAGGAGGTGGCCACTGCCATCTGGGGGGCCATTATCTTGGCCAAGCTCTCCAT
CGTCCCTGTGTGGCGAGGTTATGGGGGAACAAGATGGGCAAGCCTCACATTGTCCCGTGCCAGGGGCCAGGCCGCTGTGG
TTCTGTGCTGGTGGCCTCATTCCTGCCCCCAGACGCACTGGGATCCTGTCAGCGCCTGTCCCCAAGAAGCTGCTGCTGAT
GGCTGGAACCATGACTGCTCCATCTCAGCCAGGGCTGTGCTGCTACCTTGGGGAACTTCGCCAAAGCCACCTTTGATGCC
ATCTCTAAGGCCTACAGTTAC

Alignment

ORF - retro_dord_89 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.76 %
• Parental protein coverage: 85.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  MADDA-GAAGGPGGP-GGPGLGGRGGFRGGFGSGL-RGRGRGRGRGRGRGRAARGGKAEDKEWIPVTKLG
          MADDA..AAGGPG.P..GPGLGGRGGF.GGF.SGL..GRG...GRG.GRG...RGGKAEDKEWIP..KLG
Retrocopy MADDA<HAAGGPGSP<RGPGLGGRGGFCGGFSSGL<LGRGCDCGRGQGRGHGTRGGKAEDKEWIPIAKLG

Parental  RLVKDMKIKSLEEIYLFSLPIKESEIIDFFL-GAS-LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNG
          .LVKDMKIKSLEEIYL.SL.IKESEI.DFFL.G.S...DE.LKIMP.QKQT.AGQRTRFKAFVAIG.YN.
Retrocopy CLVKDMKIKSLEEIYLSSLSIKESEIVDFFL<GGS<IQDEGLKIMPGQKQTGAGQRTRFKAFVAIGYYNS

Parental  HVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGY-WGNKIGKPHTVPCKVTGRCGSVLVR-LIPAPRGTG
          HVGLGV.C.KEVATAI.GAIILAKLSIVPV.RGY.WGNK.GKPH.VPC...GRCGSVLV..LIPAPR.TG
Retrocopy HVGLGVQCAKEVATAIWGAIILAKLSIVPVWRGY<WGNKMGKPHIVPCQGPGRCGSVLVA<LIPAPRRTG

Parental  IVSAPVPKKLLMMAGI-DDCYTSAR-GCTATLGNFAKATFDAISKTYSY
          I.SAPVPKKLL.MAG...DC..SAR.GC.ATLGNFAKATFDAISK.YSY
Retrocopy ILSAPVPKKLLLMAGT<HDCSISAR<GCAATLGNFAKATFDAISKAYSY

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_89 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 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Dipodomys ordii	ENSDORG00000007375	18 retrocopies	retro_dord_163, retro_dord_206, retro_dord_215, retro_dord_284, retro_dord_392, retro_dord_445, retro_dord_465, retro_dord_499, retro_dord_500, retro_dord_505, retro_dord_568, retro_dord_571, retro_dord_572, retro_dord_683, retro_dord_703, retro_dord_711, retro_dord_723, retro_dord_89 ,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,