RetrogeneDB ID: retro_dord_703

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5880:10727..11607(+)
• 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_703
ATGGTGGATGATGCTGGTGCAGCAGGATGGCCCGGAGGTCCCGGGGGCCCGGGCTTGGGAGGCCTTGGAGGCTTCAGTGG
AGTCTTCGGTAGCAGCCTCCTGGGTCCCGGGTCGAGGTCACAGCCATGGTAGAGGCCAGGGTCCCGGCCACGGGGCTCGT
GGAGGCAAGGCCAAAGACGAGGAATAGATCCCCGCCACCAAACTGGGCCGCCTGGTTAAGGACATGAAGATCAAGTCTTT
GGAGGAGATCTGTCTTTCCTCCCTGTCCATCAAGGAGTCTGAGATTATTGACTTCTTCCTGAGGGCGTCACTCAAGGATG
ACGGGTTGAAGATTATGCCCGTGCAGAAGCAGACTCAAGCTGGACAGCGCACCAGGTTCAAGGCATTCGTAGCCACTGGC
GACTGCAACAGCCATGTTGGTCTGGGGGTTCAGTGCGCCAAGGAGGTGGCCACTGCCATCCGGGGCATCATCTTGGCCAA
GCTCTCCATTGTCCCCATGCAGCGGGGTTAACTGGGGGAACAAGATGGGCAAGCCTCACACTGTCCCGTGCAAGGTGACA
GGCCTCTGCGGTTCTGGGCTCGTGCGCCTCATTCCTGCCCCCAGAGGCTCTGGGATCGTTCAGCTCCTGTCCCCAAGAAG
CTGCTGCTGCTGTTTGGAATCGATGAGTGCTACACCTCAGCCAGGGGCTGTCCTGCTACCTTGGAGAATTTCCCCAAAGC
CGCCTTTGATGCCATCTCTAAGACCTACAGTTATCTGACCCCTGACCTCTGGAAAGAGACCGTATTCACCAAATCTCCTT
ATCAGGAATTCACTGCCCATCTTGTGAAAACCCACACCAGAGTCTCCGAGCAGAGGACCCAGACTTCAGCTGTGGCTACA

Alignment

ORF - retro_dord_703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 99.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGPGGPGLGGRGGFRGGFGSGLRG-RGRG--RGRGRGRGRAARGGKAEDKEWIPVTKLG
          M.DDAGAAG.PGGPGGPGLGG.GGF.G.FGS.L.G..GRG...GRG.G.G..ARGGKA.D.E.IP.TKLG
Retrocopy MVDDAGAAGWPGGPGGPGLGGLGGFSGVFGSSLLG>PGRGHSHGRGQGPGHGARGGKAKDEE*IPATKLG

Parental  RLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHV
          RLVKDMKIKSLEEI.L.SL.IKESEIIDFFL.ASLKD..LKIMPVQKQT.AGQRTRFKAFVA.GD.N.HV
Retrocopy RLVKDMKIKSLEEICLSSLSIKESEIIDFFLRASLKDDGLKIMPVQKQTQAGQRTRFKAFVATGDCNSHV

Parental  GLGVKCSKEVATAIRGAIILAKLSIVPVRRG-YWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIV-
          GLGV.C.KEVATAIRG.IILAKLSIVP..RG..WGNK.GKPHTVPCKVTG.CGS.LVRLIPAPRG.GIV.
Retrocopy GLGVQCAKEVATAIRG-IILAKLSIVPMQRG>NWGNKMGKPHTVPCKVTGLCGSGLVRLIPAPRGSGIV<

Parental  SAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVK
          SAPVPKKLL...GID.CYTSARGC.ATL.NF.KA.FDAISKTYSYLTPDLWKETVFTKSPYQEFT.HLVK
Retrocopy SAPVPKKLLLLFGIDECYTSARGCPATLENFPKAAFDAISKTYSYLTPDLWKETVFTKSPYQEFTAHLVK

Parental  THTRVSVQRTQAPAVAT
          THTRVS.QRTQ..AVAT
Retrocopy THTRVSEQRTQTSAVAT

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_703 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,