RetrogeneDB ID: retro_dord_394

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_159636:445..932(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000005292
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000003705
• Aliases: None
• Description: None

Sequence

>retro_dord_394
ATGGTCAATCCCACCATGTTCTTCGACATTGCCGCCGACGGCAAGCCCTTGGGCCGCGTCTGCTTCGAGCTGTTTGCAAA
GTTCCAAAGACAGCAGAAAACTTTCGTGCTCTGAGCACTGGAGAGAAAGGATTTGGTTATAAGGGTTCCTGCTTTCATGG
GATTATCCCAGGATTCATGTGCCAGGGTGGTGACTTTACATGCCATAATGGCACTGGTGGAAAGTCCATCTACGGAGAGA
AATTTGAGGATGAGAACTTCATCCTGAAGCATACAGGTCCTAGCATCTTGTCCATGGCACATGCTGGACCAAACACAAAT
GGTTCCCAGTTTTTCATCTGCACTGTCAAGACTGATTGCTTGGCAGCAAGCATGTGGTCTTTAGGAAGGTGAAAGAGGGC
ATGGAAGTCGTGGAAGCCATGCGGGGCTTTGGGTCCAGGAATGGCAAGCCCAGCAAGAAGGTCACCATTACCGACTGCGG
ACAACTC

Alignment

ORF - retro_dord_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVNPTVFFDIAADGKPLGRVCFELFADKVPKTAENF-RALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTC
          MVNPT.FFDIAADGKPLGRVCFELFA.K.......F.RALSTGEKGFGYKGSCFH.IIPGFMCQGGDFTC
Retrocopy MVNPTMFFDIAADGKPLGRVCFELFA-KFQRQQKTF<RALSTGEKGFGYKGSCFHGIIPGFMCQGGDFTC

Parental  HNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTVKTD-WLDGKHVVFGKVKEGMEV
          HNGTGGKSIYGEKFEDENFILKHTGP.ILSMA.AGPNTNGSQFFICTVKTD..L..KHVVF.KVKEGMEV
Retrocopy HNGTGGKSIYGEKFEDENFILKHTGPSILSMAHAGPNTNGSQFFICTVKTD<LLGSKHVVFRKVKEGMEV

Parental  VEAMQGFGSGNGKTSKKVTITDCGQL
          VEAM.GFGS.NGK.SKKVTITDCGQL
Retrocopy VEAMRGFGSRNGKPSKKVTITDCGQL

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_394 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 4 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011597	12 retrocopies	retro_chof_1071, retro_chof_1276, retro_chof_1317, retro_chof_1335, retro_chof_1876, retro_chof_1955, retro_chof_1959, retro_chof_2687, retro_chof_336, retro_chof_632, retro_chof_652, retro_chof_929,
Dipodomys ordii	ENSDORG00000003705	12 retrocopies	retro_dord_101, retro_dord_107, retro_dord_150, retro_dord_181, retro_dord_183, retro_dord_319, retro_dord_394 , retro_dord_446, retro_dord_46, retro_dord_518, retro_dord_537, retro_dord_585,
Monodelphis domestica	ENSMODG00000016089	9 retrocopies	retro_mdom_1373, retro_mdom_1524, retro_mdom_1856, retro_mdom_1884, retro_mdom_215, retro_mdom_272, retro_mdom_29, retro_mdom_730, retro_mdom_85,
Sorex araneus	ENSSARG00000007250	1 retrocopy	retro_sara_484,