RetrogeneDB ID: retro_dord_284

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_823:22517..23329(-)
• Located in intron of: ENSDORG00000010252

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_284
ATGGCAGATGATGCAGATACAACGGAAAGGACCCCAGGACCTGGAGGCCCAGGCTTGAGAGGTCGTAGTGGCTTCAGTAG
TGGCCTCCAGGATCGAGGTCCCAACTATGGTAGAGGCCAGGGTCACAGCCACAGAGCTCTGTGGAGGCAAGGCAGAAGGA
AGACAAGGAATGGATCCCCATCACCAAAGTAGGGTGCCTGGTTAAGGACATGAAGATCAACTCTTTGGAGGAGATCTATC
TTTTCTCCTTGCCCATCAAGAAGTCTGGGATTACTGACTTCTTTCTGGGGTCACTCAAGGATGAGTTGTTGAAGATTATG
CCTGTGCAGAAGCAGACTCGAGCTGACCAGTGCACCAGATTCAAGACATTTGTAGCCTTTGGTGATTACAATGGTCATTG
TCAGTCTGGGTGTTAAGTCCTACAAGGAAGTTGCCATTGGCATCCAAGGGGCCATCTTCTTGGCCAGGCTCTCCATTTTC
CCTGTATGGAGAGGTTACTAGGGAAACCAGATTGGCAAGCCTTACACTGTCCCCTGCAAGGTGACAGGCCATGCAGTTCT
GTGCTAGTGCACCTTATCCTCACCCCCAGAGGCACTGGGATCGTGTCAACTTCTGTCCCCAAGATGCTGTTGATGATGGC
TAGTATCCATGACTGCTACACCTCAGCCAAGAGCTGTATCTTGGGCTACTTAGCCACCTTTGATGCCATCTCCAAGACCT
ACAGTTACCTGACCTCTGACCTCTGGAAAGAGACCATGTTCACCAGATCTCCTTATCAGGAATTCATGGACCATCTTGTG
AAGACCCAGAGT

Alignment

ORF - retro_dord_284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.67 %
• Parental protein coverage: 94.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGPGGPGLGGRGGFRGGFGSGLRGRGRGRGRGRGRGRAA--RGGKA-EDKEWIPVTKLG
          MADDA.......GPGGPGL.G....R.GF.SGL..RG...GRG.G....A..R.G...EDKEWIP.TK.G
Retrocopy MADDADTTERTPGPGGPGLRG----RSGFSSGLQDRGPNYGRGQGHSHRALWRQGRR<EDKEWIPITKVG

Parental  RLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGH-
          .LVKDMKI.SLEEIYLFSLPIK.S.I.DFFLG.SLKDE.LKIMPVQKQTRA.Q.TRFK.FVA.GDYNGH.
Retrocopy CLVKDMKINSLEEIYLFSLPIKKSGITDFFLG-SLKDELLKIMPVQKQTRADQCTRFKTFVAFGDYNGH>

Parental  VGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGR-CGSVLVRLIPAPRGTGIV
          V.LGVK..KEVA..I.GAI.LA.LSI.PV.RGY.GN.IGKP.TVPCKVTG..C.SVLV.LI..PRGTGIV
Retrocopy VSLGVKSYKEVAIGIQGAIFLARLSIFPVWRGY*GNQIGKPYTVPCKVTGH<CSSVLVHLILTPRGTGIV

Parental  SAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVK
          S..VPK.LLMMA.I.DCYTSA..C...LG..A..TFDAISKTYSYLT.DLWKET.FT.SPYQEF.DHLVK
Retrocopy STSVPKMLLMMASIHDCYTSAKSC--ILGYLA--TFDAISKTYSYLTSDLWKETMFTRSPYQEFMDHLVK

Parental  THT
          T..
Retrocopy TQS

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_284 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,