RetrogeneDB ID: retro_dord_543

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_29572:10610..11705(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Strbp
• Ensembl ID: ENSDORG00000012137
• Aliases: None
• Description: spermatid perinuclear RNA binding protein [Source:MGI Symbol;Acc:MGI:104626]

Sequence

>retro_dord_543
AATGTTTCGATGAAAGATCCTCCAGACTTACTGGACAGGCAAAAATGCCTGAACGCCTTGGCGTCTCTTCGACATGCCAA
ATGGTTTCAGGCAAGGGCAAATGGATTAAAATCATGTGTAATTGTCCTCTGAATTCTGCGTGATTTGTGCAACAGAGTCC
CCACGTGGGCACCACTGAAAGGATGGCCACTAGAGCTTATATGTGAAAAGTCTATAGGTACTTGTAATAGACCTTTGGGC
GCTGGGGAGGCCTTGAGACAAGTAATGGAGTGTTTGGCATCTGGAATACTACTTCCTGGAGGCCCTGGTCTTCATGATCC
TGTGAGCGAGACCCAACAGATGCTCTGAGCTATATGACTATCCAACCAAAAAGAAGATATTACCCACAATGCACAGCATG
CACTTAGACTGTCAGTGTTTGGCCAGATTTATAAAGTGTTGGAGATGGACCCCCTTCCCTCTAGTAAGCCTTTTCAGAAG
TATTCCTGGTCAGTTACTGATAAAGAAGGTGCTGGGTCATCAGCTATAAAGAGGCCATTTGAAGATGGGTTAGGGGATGA
TAAAGATCCCAATAAGAAGATGAAACGAAACTTAAGAAAAATCCTGGATAGTAAAGCAAGAGACCTTATGAATGCATTAA
TGAGGCTAAATCAGATCAGACCTGGGCTTCAGTATAAGCTCTTGTCTCAGTCTGGCCCTGTCCATGCCCCAGTCTTCACA
ATGTCTGTAGATGTGGATGGCACAACTTATGAAGCCTCAGGACCATCCAAGAAAACAGCAAAACTTCACGTAGCAGTGAA
GGTTTTACAGGCAATGGGATACCCAACAGGCTTTGATGCAGATATTGAATGTATGAGTTCTGATGAAAAGTCAGACAATG
AAAGCAAAAATGAAACAGTGTCTTCAAACTCAAGCAATAATACTGGAAATTCTACAACTGAAACCTCCAGTACCTTAGAG
GTAAGAACTCAGGGCCCTATCCTCACAGCAAGTGGCAAAAATCCTGTCATGGAGCTCAATGAAAAAAGAAGAGGTCTCAA
GTATGAACTTATCTCAGAAACTGGTGGAAGCCATGATAAGCGCTTTGTAATGGAG

Alignment

ORF - retro_dord_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.82 %
• Parental protein coverage: 54.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NVSMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVLRILRDLCNRVPTWAPLKGWPLELICEK
          NVSMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVL.ILRDLCNRVPTWAPLKGWPLELICEK
Retrocopy NVSMKDPPDLLDRQKCLNALASLRHAKWFQARANGLKSCVIVL*ILRDLCNRVPTWAPLKGWPLELICEK

Parental  SIGTCNR-LGAGEALRRVMECLASGILLPGGPGLHDP-CERDPTDALSYMTIQ-QKEDITHSAQHALRLS
          SIGTCNR.LGAGEALR.VMECLASGILLPGGPGLHDP.CERDPTDALSYMTIQ.QKEDITH.AQHALRLS
Retrocopy SIGTCNRPLGAGEALRQVMECLASGILLPGGPGLHDP<CERDPTDALSYMTIQ>QKEDITHNAQHALRLS

Parental  AFGQIYKVLEMDPLPSSKPFQKYSWSVTDKEGAGSSAIKRPFEDGLGDDKDPNKKMKRNLRKILDSKAID
          .FGQIYKVLEMDPLPSSKPFQKYSWSVTDKEGAGSSAIKRPFEDGLGDDKDPNKKMKRNLRKILDSKA.D
Retrocopy VFGQIYKVLEMDPLPSSKPFQKYSWSVTDKEGAGSSAIKRPFEDGLGDDKDPNKKMKRNLRKILDSKARD

Parental  LMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGF
          LMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGF
Retrocopy LMNALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGYPTGF

Parental  DADIECMSSDEKSDNESKNETVSSNSSNNTGNSTTETSSTLEVRTQGPILTASGKNPVMELNEKRRGLKY
          DADIECMSSDEKSDNESKNETVSSNSSNNTGNSTTETSSTLEVRTQGPILTASGKNPVMELNEKRRGLKY
Retrocopy DADIECMSSDEKSDNESKNETVSSNSSNNTGNSTTETSSTLEVRTQGPILTASGKNPVMELNEKRRGLKY

Parental  ELISETGGSHDKRFVME
          ELISETGGSHDKRFVME
Retrocopy ELISETGGSHDKRFVME

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_543 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000012137	1 retrocopy	retro_dord_543 ,
Felis catus	ENSFCAG00000004095	1 retrocopy	retro_fcat_38,