RetrogeneDB ID: retro_dord_505

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_24425:4623..5477(+)
• Located in intron of: None

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_505
GCAGGAGGGTCTGGAGGTCACAGGGGCCCGGGCTTGGGAGGCCATGGCGGCTTCCGTGGAGGCTTCCTTAGCGGCCTCAG
GGGCCGAGGTCATGGCCGTGGTAGAGGCCGGGCCCTGGGGCTCGCAAGGAAAAAGACAAGGAATGGCTCCCCGTCACCAA
ACTGGGCCCTCTGGTTAAGGACATGAAGATCAAGTCTCTGGAGGAGATCTACCTTTTCTCCCTGCCCATCAAGGAGTCTG
AGATTGTCTAAGAAGTCTAGGACTTCTTCCTGGGGCATCACTCAAAGATGAGGGGGTTGAAGATTATGCCCGTGCAGAAG
CAAATTCGAGCTGGCCAGCGCACCAGGTTCAAGGCATTCGTAGCCATTGGCAACTGCAATGGCCATGTTGGTCTGGGGGT
TAAGTGCGCCAAGGAGGTGGCCACTGCCATGCGGGGGGCATCATCTTGGCTAAGCTCTCCATCATCCTGTGCGGCGAGGT
TAATGGGGGGACAGGATTGGCAAGCCTCACCCTGTCCCGTGCAAGGTGACAGGCTGCTGTGGTTCTGTGCTCGTGCGCAT
CATTCCTGCCCCCAGAGGCACTGGGATTGTGTCAGCTCCTGTCGCCAAGAAGCTGCTGCTGATGTCTGGCATCCATGACT
GCTCCACCTCAGCCAGGGGCTGTGCTGCTACCTTGGGGAACTTGGCCAAAGCCACCTTTGATGCCATCTCTAAGACCTAT
AGCACCTGACCCCTGACCTCTGGAAAGAGACCATATTCACCAAATCTCCTTATCAGGAATTCACTGACCATCTCGTGAAA
ACCCACACCAGGGTCTGTGTGCAGAGGACCCAAGCTCCAGCTGTGGCTACAACA

Alignment

ORF - retro_dord_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.11 %
• Parental protein coverage: 97.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AGGPGGPGGPGLGGRGGFRGGFGSGLRGRGRGRGRGRGR-GRAARGGKAEDKEWIPVTKLGRLVKDMKIK
          AGG.GG..GPGLGG.GGFRGGF.SGL..RGRG.GRGRGR.G..AR..K..DKEW.PVTKLG.LVKDMKIK
Retrocopy AGGSGGHRGPGLGGHGGFRGGFLSGL--RGRGHGRGRGR<GPGAR--KEKDKEWLPVTKLGPLVKDMKIK

Parental  SLEEIYLFSLPIKESEII----DFFLG-ASLKDEV-LKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
          SLEEIYLFSLPIKESEI.....DFFLG.ASLKDE..LKIMPVQKQ.RAGQRTRFKAFVAIG..NGHVGLG
Retrocopy SLEEIYLFSLPIKESEIV*EV*DFFLG<ASLKDEG>LKIMPVQKQIRAGQRTRFKAFVAIGNCNGHVGLG

Parental  VKCSKEVATAIRGA-IILAKLSIV-PVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAP
          VKC.KEVATA.RGA.IILAKLSI..PVRRG.WG..IGKPH.VPCKVTG.CGSVLVR.IPAPRGTGIVSAP
Retrocopy VKCAKEVATAMRGA<IILAKLSII<PVRRG*WGDRIGKPHPVPCKVTGCCGSVLVRIIPAPRGTGIVSAP

Parental  VPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYS-YLTPDLWKETVFTKSPYQEFTDHLVKTH
          V.KKLL.M.GI.DC.TSARGC.ATLGN.AKATFDAISKTYS..LTPDLWKET.FTKSPYQEFTDHLVKTH
Retrocopy VAKKLLLMSGIHDCSTSARGCAATLGNLAKATFDAISKTYS<HLTPDLWKETIFTKSPYQEFTDHLVKTH

Parental  TRVSVQRTQAPAVATT
          TRV.VQRTQAPAVATT
Retrocopy TRVCVQRTQAPAVATT

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_505 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,