RetrogeneDB ID: retro_dord_465

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_20351:17402..18201(+)
• 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_465
AGTGGGAAGACTGGGAGGCCCCAGGGCCCTGGTTTGGGGGGCCATGGTGGCTTCCAAGGAGGAGCCGCAGCAGCCTCTGA
GAAAAAGGCAAGGAACAGATCCCCAGCCCCCTACTAGGCCGCCCAGTTAAGGACATGAAGATCAAGTCTTGGGAGGAGAT
CTATCGTTCCTCCCTGCTCATCAAGGAGTCTGAGACTATTGACTTCTTCCAGGGGTCACTCAAGGATGAGGTGTTGAAGA
TTATGCCCAGAAGCAGACTGAGCTGAGCTGGCCGGCGCACCGGCTTCAAGGCATTTGAAAATGTAGCCATTGGCTACCAC
CATGGCCATGTCAGTCTGCATGTTAAGTGCTCCCAGGGGGTTGTCACTGCCATGCAAGAGGCCACCATCTTGGCCAAACT
CTCTGTTATCCCTGTGCGGAGAGGCTACTGGGGGAACAAGACTGGCAAGCCCCACCCTGTCCCCGGCGAGGTGACAGGCC
GCTGAGGTTCTGCGCTGGTGGCCTCATCCTCGTCCCCAGAGGCACTGGGATCTTGTCAGCTCCTGTCCCCAAGAAGCGGG
GGCTGGTGGCTGGTATGGATGTCTGCTACACCTCAGCCAGGAGCTGTGCTGCCACCTAGGCCAACTTCACCAAGACCACC
TTTGATGCCATCTCTAAGACCTACAGTCACCTGATCCCTAACCTCTGGAAGGAGACCGTGTGCACCAAATCTCCTTTTCA
GGAATTCACTGACCATCTTATGAAAACCCACACCAGAGCCTCCATGCAGAGGACCCAGGCTCCAGCTGTGGCTACAACA

Alignment

ORF - retro_dord_465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.41 %
• Parental protein coverage: 89.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGLRGRGRGR---GRGRGRGRAARGGKAE-DKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDF
          SG..GR..G....G.G...G.AA........KE.IP...LGR.VKDMKIKS.EEIY..SL.IKESE.IDF
Retrocopy SGKTGRPQGPGLGGHGGFQGGAAAASEKK<GKEQIPSPLLGRPVKDMKIKSWEEIYRSSLLIKESETIDF

Parental  FLGASLKDEVLKIMPVQKQTRAGQRTRFKAF--VAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVP
          F.G.SLKDEVLKIMP......AG.RT.FKAF..VAIG...GHV.L.VKCS..V.TA...A.ILAKLS..P
Retrocopy FQG-SLKDEVLKIMPRSRLS*AGRRTGFKAFENVAIGYHHGHVSLHVKCSQGVVTAMQEATILAKLSVIP

Parental  VRRGYWGNKIGKPHTVPCKVTGRCGSVLVR-LIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATL
          VRRGYWGNK.GKPH.VP..VTGR.GS.LV..LI..PRGTGI.SAPVPKK....AG.D.CYTSAR.C.AT.
Retrocopy VRRGYWGNKTGKPHPVPGEVTGR*GSALVA<LILVPRGTGILSAPVPKKRGLVAGMDVCYTSARSCAAT*

Parental  GNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT
          .NF.K.TFDAISKTYS.L.P.LWKETV.TKSP.QEFTDHL.KTHTR.S.QRTQAPAVATT
Retrocopy ANFTKTTFDAISKTYSHLIPNLWKETVCTKSPFQEFTDHLMKTHTRASMQRTQAPAVATT

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_465 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,