RetrogeneDB ID: retro_dord_754

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_7662:50249..51338(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sppl2a
• Ensembl ID: ENSDORG00000008946
• Aliases: None
• Description: signal peptide peptidase like 2A [Source:MGI Symbol;Acc:MGI:1913802]

Sequence

>retro_dord_754
GCTGCTCAGGAAGCAGTTCTGCGTGCATCTGGAAGCGGCACCCCTTTACCCTCCAAGGACTACTGCATGCTATATCATCC
TCTTTGGACAGTGCTTCCAACTACCCTAGAAAATGCAACTTCCAGAAGTCTGATGGATCTTACTGGCACACCACTATGCA
AGCTTTCTGATCTTCCTCTCCATGGCATGAACAATAAAGCAGTTGTGGTACAGTGGGGACCCTGCCATTTTCTGGAAAAA
GCCAGAATTGCACAGAAAGGGGGTGCTGATGCATTGTTGGTTGCCAATAACAGTGTTCTCTTTCGTCCCTCAGGGAATAG
ATCTGAATTTCAAGATGTGAAAATACCAATTGCATTTATAAGCCAAAAAGACTTTAAAGACATGAAACAGACTTTTGGAA
GTAACATTACTGTAAAAATGTACTTACCACCACAGCCTGACTTTGACTATACAATGGTGGTTATTTTTGTAATTTCTGTG
TTCACTGAGGCATTAGGAGGATACTGGAGTGGACTTTATTGAATTAGAAAACTTAAAGACAATAACAAGCGCCGAGAAAG
AGAAATGAGGAAAAAGAAGGAAGAATATGTAACTTTCAGTCCTCTTACAGTTGTAGTATTTGTGGTCATCTGCTGTGTTA
TGATGGTCTTACTGTATTTCTTCTATAAGTAGTTGGTTTATGTTATAATAGCAATATTCTGCATAGCATCAGCAATGAGT
CTGTACAACTGTCTTGCTGCACTAATTCATAAGATACCATGTGGACAATGCACGATTACATGTCGTGGCAAAAGCATTGA
AGTGAGACTTATTTTTCTCTCTGGACTATGCATAGCTGTAGCTGTTGTTTGGGCTGTGTTTAGAAATGAGGATAGGTGGT
TTTGGATATTACAGGATATCTTGGGCATTGCTTTCTGCCTCAATTTAATTAAAACACTGAAGTTACCCAACTTCAAGTCA
TGTGTGATACTTCTAGGCCTTCTCCTCCTCTATGATGTTTTTTTTGTTTTCATAACACCATTCATCACAAAGAATGGTGA
GAGTATTATGGTTGAACTTGCAGCTGGACCTTTTGGAAACACAGAAAAG

Alignment

ORF - retro_dord_754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.97 %
• Parental protein coverage: 72.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAQEAVLHASGSGTPLPSKDYCMLYNPLWTVLPTTLENATSRSLMDLTSTPLCNLSDLPLHGMNNKAVVV
          AAQEAVL.ASGSGTPLPSKDYCMLY.PLWTVLPTTLENATSRSLMDLT.TPLC.LSDLPLHGMNNKAVVV
Retrocopy AAQEAVLRASGSGTPLPSKDYCMLYHPLWTVLPTTLENATSRSLMDLTGTPLCKLSDLPLHGMNNKAVVV

Parental  QWGPCHFLEKARIAQKGGADALLVANNSVLFRPSGNRSEFQDVKIPIAFISQKDFKDMKQTLENN-TVKM
          QWGPCHFLEKARIAQKGGADALLVANNSVLFRPSGNRSEFQDVKIPIAFISQKDFKDMKQT...N.TVKM
Retrocopy QWGPCHFLEKARIAQKGGADALLVANNSVLFRPSGNRSEFQDVKIPIAFISQKDFKDMKQTFGSNITVKM

Parental  FIPPRPDFDYTMVVIFVISVFTVALGGYWSGL-IELENLKTITSTE-EREMRKKKEEYVTFSPLTVVVFV
          ..PP.PDFDYTMVVIFVISVFT.ALGGYWSGL.IELENLKTITS.E.EREMRKKKEEYVTFSPLTVVVFV
Retrocopy YLPPQPDFDYTMVVIFVISVFTEALGGYWSGL>IELENLKTITSAE<EREMRKKKEEYVTFSPLTVVVFV

Parental  VICCVMMVLLYFFYKWLVYVIIAIFCIASAMSLYNCLAALIHKIPCGQCTITCRGKSIEVRLIFLSGLCI
          VICCVMMVLLYFFYK.LVYVIIAIFCIASAMSLYNCLAALIHKIPCGQCTITCRGKSIEVRLIFLSGLCI
Retrocopy VICCVMMVLLYFFYK*LVYVIIAIFCIASAMSLYNCLAALIHKIPCGQCTITCRGKSIEVRLIFLSGLCI

Parental  AVAVVWAVFRNEDRWAWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDVFFVFITPFITKNGES
          AVAVVWAVFRNEDRW.WILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYD.....ITPFITKNGES
Retrocopy AVAVVWAVFRNEDRWFWILQDILGIAFCLNLIKTLKLPNFKSCVILLGLLLLYDXXXXXITPFITKNGES

Parental  IMVELAAGPFGNTEK
          IMVELAAGPFGNTEK
Retrocopy IMVELAAGPFGNTEK

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_754 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008946	1 retrocopy	retro_dord_754 ,
Homo sapiens	ENSG00000138600	1 retrocopy	retro_hsap_1566,
Gorilla gorilla	ENSGGOG00000013154	1 retrocopy	retro_ggor_1191,
Pongo abelii	ENSPPYG00000006472	1 retrocopy	retro_pabe_1293,
Pan troglodytes	ENSPTRG00000007070	1 retrocopy	retro_ptro_1054,
Rattus norvegicus	ENSRNOG00000011652	1 retrocopy	retro_rnor_1750,