RetrogeneDB ID: retro_dord_254

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6786:46199..47338(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000015889
• Aliases: None
• Description: None

Sequence

>retro_dord_254
ATGAGGGAGATTGTGTACATACAGGCAGGCCTGTGTGGCAACCAGATTGGCGCAAAGTTTTGGGAAATGCTAAGCGATGA
GCACAACATTGACTGCACTGGCAACTACTATGGAGACAGCAGCTTACAGCTGCAGAGAATCGAGGTGTATTACAATGAGG
CAGCTGGCAACAAATATGTTCCTCAGGCCATCATGGTGTACCTAGAGCCTGGCACCTTAGACTCAGTGAGATCGGGACCA
TTTGGCTAGAGCTTTAGGCCAGACAACTTCATATTTGGCCAGAGCAGGGCAGGCAATAACTGGGCCAAGGGCCACTACAC
AGAGAGAGTCGAGCTGGTGGAGTCGGTGTTGGATGTAGTGTGGTGGGAGTCAGAAAGGTGTGACTGTCTCTAGGGTTTCC
AGCTGGCCCACTCCATGGGAGGTGGCACCAGGTCAGGCATGATGCTCAACAAGATCTGAGAGGAGTACCCAGACCACATC
ATGAACACCTTCAGTGTCATGCCCTCCCCCAAAGTGTCAGAACCGTGGTGGAACCCTACAACACGATCTTGTCTGTCCAC
CAGTTGGTGGAAAATGCAGATGAAGCTTTCTGCATCGACAAAGAGGCCCTGTAGGACACCTGCTTCCACACCATGAAGCT
GCCCACGCCCACCTATGGAGACCTGAACCACCACCTGGTGTCAGCAACCATGAGCATGGTCACCACCTGCCTGTGCTTCC
CCGGCCAGCTGAATGCAGACTTGTGCAACCTGGCCGTGAATATGGTGCCCTTCCCCCGCCTGCACTTCTTCATGCCTGGC
TTTGCGCCCCTGACAAGCAGTGCCAGCCAGCAGTACCATGCTCTCTCAGTGCCCAAGCTCACCAGCAGATGTTTTGACAC
CAAGAACATGATGGTTGCCTGTGATCCCCACCATGGCCACTACCTGACAGCGGCTGCCATCTTCCGAGGCCATATGTCCA
TGAAGGACGTGGATAAGCTCAACGTGCAGAACAAGAACAGCAGCTACGTTGCAGACTGGATCCCCAACAACATGAAGACG
GCTGTGTGTGACATCCCTCCTCATGGCCTCACGATGTCAGCCACCTTCATCGTCAACAACTCGGCCATCCAGGATCCCTT
CAAGTGCACCCAGCGCAAA

Alignment

ORF - retro_dord_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 86.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREIVYIQAGQCGNQIGTKFWEMISDEHNIDCTGNYYGDSHLQLQRIEVYYNEATGNKYVPRAIMVDLEP
          MREIVYIQAG.CGNQIG.KFWEM.SDEHNIDCTGNYYGDS.LQLQRIEVYYNEA.GNKYVP.AIMV.LEP
Retrocopy MREIVYIQAGLCGNQIGAKFWEMLSDEHNIDCTGNYYGDSSLQLQRIEVYYNEAAGNKYVPQAIMVYLEP

Parental  GTLDSVRSGPFGQSFRPDNFIFGQSGAGNNWAKGHYTEGAELLESVLDVVRRESERCDCLQGFQLAHSLG
          GTLDSVRSGPFG.SFRPDNFIFGQS.AGNNWAKGHYTE..EL.ESVLDVV..ESERCDCL.GFQLAHS.G
Retrocopy GTLDSVRSGPFG*SFRPDNFIFGQSRAGNNWAKGHYTERVELVESVLDVVWWESERCDCL*GFQLAHSMG

Parental  GGTGSGMGTLILNKIREEYPDRIMNTFSVMPSPKVSD-TVVEPYNAILSVHQLVENADETFCIDNEALYD
          GGT.SGM....LNKI.EEYPD.IMNTFSVMPSPKVS..TVVEPYN.ILSVHQLVENADE.FCID.EAL.D
Retrocopy GGTRSGM---MLNKI*EEYPDHIMNTFSVMPSPKVSE<TVVEPYNTILSVHQLVENADEAFCIDKEAL*D

Parental  ICFRTLKLPTPSYGDLN-HLVSATMSGVTTCMRFPGQLNADLRKLAVNMVPFPRLHFFMTGFAPLTSRAS
          .CF.T.KLPTP.YGDLN.HLVSATMS.VTTC..FPGQLNADL..LAVNMVPFPRLHFFM.GFAPLTS.AS
Retrocopy TCFHTMKLPTPTYGDLNHHLVSATMSMVTTCLCFPGQLNADLCNLAVNMVPFPRLHFFMPGFAPLTSSAS

Parental  QQYHVLSVPELTQQMFDAKNMMVACDPHHGRYLTAAAIFRGRMSMKELDEQMFNMQNKNSSYFADWIPNN
          QQYH.LSVP.LT...FD.KNMMVACDPHHG.YLTAAAIFRG.MSMK..D....N.QNKNSSY.ADWIPNN
Retrocopy QQYHALSVPKLTSRCFDTKNMMVACDPHHGHYLTAAAIFRGHMSMKDVDK--LNVQNKNSSYVADWIPNN

Parental  VKTAVCDIPPRGLTMSATFIGNNTAIQEPFKRTSEQ
          .KTAVCDIPP.GLTMSATFI.NN.AIQ.PFK.T...
Retrocopy MKTAVCDIPPHGLTMSATFIVNNSAIQDPFKCTQRK

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_254 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284,
Dipodomys ordii	ENSDORG00000015889	1 retrocopy	retro_dord_254 ,
Homo sapiens	ENSG00000173213	1 retrocopy	retro_hsap_3733,
Homo sapiens	ENSG00000173876	1 retrocopy	retro_hsap_3944,
Mus musculus	ENSMUSG00000016255	1 retrocopy	retro_mmus_1109,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250,