RetrogeneDB ID: retro_dord_638

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_4494:63154..63742(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sae1
• Ensembl ID: ENSDORG00000012199
• Aliases: None
• Description: SUMO1 activating enzyme subunit 1 [Source:MGI Symbol;Acc:MGI:1929264]

Sequence

>retro_dord_638
CTGCGGACCTCCCGGGTGCTGGTGGTTGGAATGATGGGACTGGGAGCCGAAATCACCAAGAACCTCATCCTGGCTGGAAT
GAAAGGGCCGACCAAGCTGGACCACAAATTGGTGTCTGCGGAACATCCTGGAGCGCAGTTTCTGGTTCGTACTGGGTCTG
TTGGACGAAATAGAGCCGAAGCCTCTTTGGAGCGAGCTCAGAATCTTAACCCCATGGTGAATATGAAGGTGGACACAGAG
GACATAGAGAAGAAAACAGAGTCACTTTTCACTCAGTTTGGTGCTATGTGCCTGGCTGGTTGCTCAAGGGATGTCATCAT
TAATGTTGACCAGATCTGCCACAAAAACAGCATCAAGTGCTTCACCGGAGAGGTCTTTGGCTATCATGGTTACACATTTG
CCAATCTTGGAGAGCATGAGTTTGTTGAGGAGAAAACCAAAATTGTCAAAGTTAGCCAAGGAGTGGAAGATGGGCCTGAC
ACCAAAAAGGCAAAACTTGACTCATCTGAGACAACAATGGTGAAGAAGAAGATGGTTTTCTGCCCCATCAAAGAGGCCCT
GGCAGTAGACTGGAGCAGCGAGAAGGCC

Alignment

ORF - retro_dord_638 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.29 %
• Parental protein coverage: 62.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRTSRVLVVGMRGLGAEIAKNLILAGVKGLTMLDHELVSPEDPGAQFLIRTGSVGRNRAEASLERAQNLN
          LRTSRVLVVGM.GLGAEI.KNLILAG.KG.T.LDH.LVS.E.PGAQFL.RTGSVGRNRAEASLERAQNLN
Retrocopy LRTSRVLVVGMMGLGAEITKNLILAGMKGPTKLDHKLVSAEHPGAQFLVRTGSVGRNRAEASLERAQNLN

Parental  PMVDVKVDTEDIEKKTESFFTQFDAVCLTGCSRDVIINVDQICHKNSIKFFTGDVFGYHGYTFANLGEHE
          PMV..KVDTEDIEKKTES.FTQF.A.CL.GCSRDVIINVDQICHKNSIK.FTG.VFGYHGYTFANLGEHE
Retrocopy PMVNMKVDTEDIEKKTESLFTQFGAMCLAGCSRDVIINVDQICHKNSIKCFTGEVFGYHGYTFANLGEHE

Parental  FVEEKTKVAKVSQGVEDGPDTKKAKLDSSETTMVKKKVVFCPIKEALEVDWSSEKA
          FVEEKTK..KVSQGVEDGPDTKKAKLDSSETTMVKKK.VFCPIKEAL.VDWSSEKA
Retrocopy FVEEKTKIVKVSQGVEDGPDTKKAKLDSSETTMVKKKMVFCPIKEALAVDWSSEKA

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_638 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004180	1 retrocopy	retro_cfam_1705,
Dipodomys ordii	ENSDORG00000012199	1 retrocopy	retro_dord_638 ,
Homo sapiens	ENSG00000142230	1 retrocopy	retro_hsap_829,
Gorilla gorilla	ENSGGOG00000013078	1 retrocopy	retro_ggor_679,
Macaca mulatta	ENSMMUG00000009506	1 retrocopy	retro_mmul_1087,
Nomascus leucogenys	ENSNLEG00000002965	1 retrocopy	retro_nleu_261,
Nomascus leucogenys	ENSNLEG00000002966	1 retrocopy	retro_nleu_262,
Pongo abelii	ENSPPYG00000010168	1 retrocopy	retro_pabe_742,
Pan troglodytes	ENSPTRG00000011202	1 retrocopy	retro_ptro_579,