RetrogeneDB ID: retro_dord_568

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_3381:73199..73816(+)
• 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_568
AGGGGCCCACGCATGGGAGACTCTGGCTGCTTCCTGGGAGGCTTTGGTAGCAGATTCTGGGGCCAAGGTCATGGCATAGG
AGCTAGTGGAGGCAAAGCCAAAGACCAGGAATGGATCCCTGCCACCAAACTGGGCCTCCTGGTTAAGGCCATGAAGATGA
AGTCTTTGGAGGAGATCTGTCTTTTCTCCCTGCCCATCAAGGAGTCTGAGATTGTTGACTTCTTCCTGGAGTCACTCAAG
GATAAGGAGTTGAGGATTGTATCCATGCAGAAGCACACCCGAGCTGGCCAGTGCACCAAGTTCAAGGCATTTGTAGACAT
TGGCAACTACAACAGCCATGGCGGTCTGGGGTTATGTGCTCCAAGGAGGCTGCCACTGCTGTCCAAGGGGTCATCATCTG
GGCCATGCTCTCCATTGTCCCTGAGACTATGGGGAACAAGGTTGGCAAGCCCCACACTGTGACATGCAAGGTGACAGGTT
CTGCACTGGTGAGCCTTATCTCCACCCACAGAGGCACTGGGATCGTGTCAGCTCCTGTCCCCAAGAAGCTGTGGATGATG
GCTGGTATTGATGACTGCTATACCTCAGCCGGGGGCTGTGCTGCTACCTTGGGCCAC

Alignment

ORF - retro_dord_568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.91 %
• Parental protein coverage: 73.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGGFRGGFGSGLRGRGRGRGRGRGRGRAARGGKAEDKEWIPVTKLGRLVKDMKIKSLEEIYLFSLPIKES
          RG...G..G..L.G.G..R..G.G.G..A.GGKA.D.EWIP.TKLG.LVK.MK.KSLEEI.LFSLPIKES
Retrocopy RGPRMGDSGCFLGGFG-SRFWGQGHGIGASGGKAKDQEWIPATKLGLLVKAMKMKSLEEICLFSLPIKES

Parental  EIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGL-GVKCSKEVATAIRGAIILAKL
          EI.DFFL..SLKD..L.I...QK.TRAGQ.T.FKAFV.IG.YN.H.GL.GV.CSKE.ATA..G.II.A.L
Retrocopy EIVDFFL-ESLKDKELRIVSMQKHTRAGQCTKFKAFVDIGNYNSHGGL<GVMCSKEAATAVQGVIIWAML

Parental  SIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCT
          SIVP...G...NK.GKPHTV.CKVTG...S.LV.LI...RGTGIVSAPVPKKL.MMAGIDDCYTSA.GC.
Retrocopy SIVPETMG---NKVGKPHTVTCKVTG---SALVSLISTHRGTGIVSAPVPKKLWMMAGIDDCYTSAGGCA

Parental  ATLGN
          ATLG.
Retrocopy ATLGH

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_568 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,