RetrogeneDB ID: retro_dord_711

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_5965:52515..53224(-)
• 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_711
GCTTGTGGAGGCAAGGCGGAAGACAAGGAATGGATCCCTGTCACCAAACTGGGCTGCCTGGTTAAGGACATGAAGACCAA
GTCTCTGGAGGAGATCTATCTTTCCTCCCCACCCATCAAGGAGATGACTGAATTCTTCCTGGGGGTGTCACTCAAAGATG
AGGTGTTGAAGATTATGCCCATGCAGAAGCAAACTCGAGCTGGCCAGGGCACTGGGTTCAAGGCATTTGTAGCCATTGGC
AACTACAACGGCCATGCTGGTTTGGGTGTTACGTGCTCCCAGGAGGTGGCCACTGCATCTGGGGGGAGCTCTCATCTTGG
CCAAGCTCTCCATCATCCCTGTGCAGTGAGGCTACTGGGGGAACACCAAGCTTCACACTGTCACCTGAAAGGTGACAGGC
CGCTGGTGCTTCATCCTGGACCCCAGAGGCATTGGGGACACCCTAGTGTCAGCTCCTGTCCCCAAGAAGCTGTTGATGGT
GGCTGGTAACCGTGATAGCTCCACCTCAGCCAGGGACTGTACTGCTACCTTGGGGAACTTCGCCAAAGCCGCCTTTGATG
CCATCTCTAAGACCTACAGTTACCTGACCCCTGACCTCTGGAAAGAGACCGTATTCACCAAATCTCCTTATCAGGAATTC
ACTGACCATCTTGTGAAAACCCACCCCAGAGTCTCCCTGCAGAGGACCCAGGCTCCAGCTGTGGCTACA

Alignment

ORF - retro_dord_711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.87 %
• Parental protein coverage: 82.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARGGKAEDKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAG
          A.GGKAEDKEWIPVTKLG.LVKDMK.KSLEEIYL.S.PIKE.....FFLG.SLKDEVLKIMP.QKQTRAG
Retrocopy ACGGKAEDKEWIPVTKLGCLVKDMKTKSLEEIYLSSPPIKE--MTEFFLGVSLKDEVLKIMPMQKQTRAG

Parental  QRTRFKAFVAIGDYNGHVGLGVKCSKEVATA-IRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRC
          Q.T.FKAFVAIG.YNGH.GLGV.CS.EVATA...GA.ILAKLSI.PV..GYWGN...K.HTV..KVTGR.
Retrocopy QGTGFKAFVAIGNYNGHAGLGVTCSQEVATA>LGGALILAKLSIIPVQ*GYWGNT--KLHTVT*KVTGRW

Parental  GSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKE
          ...L....P...G...VSAPVPKKLLM.AG..D..TSAR.CTATLGNFAKA.FDAISKTYSYLTPDLWKE
Retrocopy CFIL---DPRGIGDTLVSAPVPKKLLMVAGNRDSSTSARDCTATLGNFAKAAFDAISKTYSYLTPDLWKE

Parental  TVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVAT
          TVFTKSPYQEFTDHLVKTH.RVS.QRTQAPAVAT
Retrocopy TVFTKSPYQEFTDHLVKTHPRVSLQRTQAPAVAT

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_711 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,