RetrogeneDB ID: retro_dord_126

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3716:291826..292726(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Smu1
• Ensembl ID: ENSDORG00000006011
• Aliases: None
• Description: smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans) [Source:MGI Symbol;Acc:MGI:1915546]

Sequence

>retro_dord_126
GCATACCCAGAAGGAAGCAGCAAAGAGAAAAGAAGAGCAGCCATTGCCCAAGCCTTAGCTGGCGAAGTCAGTGTGGTACC
TCCGTCTCGTCTCTTGGCATTGCTGGGCCAGGCTCTGAAGTGGCAGCAGCACCAAGGGTTGCTCCCTCCTGGTCCCACCA
TAGATCTGTTTCGAGGTAAAGCAGCTGTCAAAGATGTGGAGGAAGAAAAGTTTCCTACACGGCTGAGCAGGCATATTAAG
TTTGGTCAGAAGTCACACGTGGAATGTGCTAGATTTTCTCCAGATGGTCAGTATCTGGTCACTGGGTCTGTTGATGGATT
TATTGAAGTATGGAACTTTATGACTGGAAAAATCAGGAAGGATCTGAAGTACCAGGCACAGGATAACTTCATGATGATGG
ACGATGCTGTCCTCTGCATGTGTTTTAGCAGAGATACAGAAATGTTAGCAACTGGGGCCCAAGATGGAAAGATCAAGGTG
TGGAAGATTCAGAGTGGACAGTGTTTAAGGAGGTTTGAAAGGGCACATAGTAAAGCTGTCACCTCTCTGAGCTTTTCCAA
AGACAGCAGTCAGATCCTTAGTGCCTCTTTGGACCAGACAATCAGAATTCATGGCTTAAAATCTGGGAAAACCCTAAAGG
AATTTTGTGGTCATTCCTCCTTCGTTAATGAAGCAACATTTACACAAGATGGACATTATATTATCAGTGCTTCCTCTGAT
GGCACTGTAAAGATCTGGAATACGAAGACAACAGAATGCTCAAATACCTTGAAATCCTTGGGCAGCACTGCGGGGACAGA
CATTACTGTCAACAGTGTGATCCTGCTTCCTAAAAACCCAGAACACTTTGTGGTGTGCAACCGATCAAACACTGTGGTCA
TCATGAACATGCAAGGCCAG

Alignment

ORF - retro_dord_126 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 69.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYPDGSSKEKRRAAIAQALAGEVSVVPPSRLMALLGQALKWQQHQGLLPPGMTIDLFRGKAAVKDVEEEK
          AYP.GSSKEKRRAAIAQALAGEVSVVPPSRL.ALLGQALKWQQHQGLLPPG.TIDLFRGKAAVKDVEEEK
Retrocopy AYPEGSSKEKRRAAIAQALAGEVSVVPPSRLLALLGQALKWQQHQGLLPPGPTIDLFRGKAAVKDVEEEK

Parental  FPTQLSRHIKFGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFTTGKIRKDLKYQAQDNFMMMDDAVLCM
          FPT.LSRHIKFGQKSHVECARFSPDGQYLVTGSVDGFIEVWNF.TGKIRKDLKYQAQDNFMMMDDAVLCM
Retrocopy FPTRLSRHIKFGQKSHVECARFSPDGQYLVTGSVDGFIEVWNFMTGKIRKDLKYQAQDNFMMMDDAVLCM

Parental  CFXXXXXXXXXXXXXXXXXVWKIQSGQCLRRFERAHSKGVTCLSFSKDSSQILSASFDQTIRIHGLKSGK
          CF.................VWKIQSGQCLRRFERAHSK.VT.LSFSKDSSQILSAS.DQTIRIHGLKSGK
Retrocopy CFSRDTEMLATGAQDGKIKVWKIQSGQCLRRFERAHSKAVTSLSFSKDSSQILSASLDQTIRIHGLKSGK

Parental  TLKEFRGHSSFVNEATFTQDGHYIISASSDGTVKXXXXXXXXXXXXFKSLGSTAGTDITVNSV-LLPKNP
          TLKEF.GHSSFVNEATFTQDGHYIISASSDGTVK.............KSLGSTAGTDITVNSV.LLPKNP
Retrocopy TLKEFCGHSSFVNEATFTQDGHYIISASSDGTVKIWNTKTTECSNTLKSLGSTAGTDITVNSVILLPKNP

Parental  EHFVVCNRSNTVVIMNMQGQ
          EHFVVCNRSNTVVIMNMQGQ
Retrocopy EHFVVCNRSNTVVIMNMQGQ

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_126 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000006011	2 retrocopies	retro_dord_126 , retro_dord_137,
Dipodomys ordii	ENSDORG00000015010	1 retrocopy	retro_dord_7,
Echinops telfairi	ENSETEG00000007953	1 retrocopy	retro_etel_1686,
Myotis lucifugus	ENSMLUG00000016097	1 retrocopy	retro_mluc_213,
Monodelphis domestica	ENSMODG00000003439	1 retrocopy	retro_mdom_965,