RetrogeneDB ID: retro_dord_517

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_25284:9106..9455(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Bcl7c
• Ensembl ID: ENSDORG00000001676
• Aliases: None
• Description: B cell CLL/lymphoma 7C [Source:MGI Symbol;Acc:MGI:1332237]

Sequence

>retro_dord_517
GAAGATGTGAGCAGCATGGAGTGACTGTGGGTGAAGCTTCACTTTCTATCTTTAAGTAGGTAAAAGTGGTGGACTACCAC
CCCCACCCCCACCCAAGAAGAGGAGAGACAGAGGGCAGGTGTGTACAGACCGATATGTGGCCAGAAGAGGAGGAGCAGGG
GCACAGTCAAGAAGAGTGGCTCTCTATCTGCTGGACTTCAACAACGACAACAGCAGCCAGAGTTTCCATTCAGAAGGTTC
CCTACAAAAAGGCACAGAGCCAAGCCCTGGGGGCACTCTTCAGCCCAGACACTCTGTGTCACTTGCTGGACTCCCAGAAG
CCCCCACAACTGGGCCAAGAGAGAGACCC

Alignment

ORF - retro_dord_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.26 %
• Parental protein coverage: 66.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKVRRWEKRWVTVGDTSLRIFKW-VPVVDPQEEERRRAGGG-TDRSRGRERRGRGASPRGGGPLILLDLN
          E.V...E..WV.....SL...KW......P..EE.R...G..TDR...R.R.G.GA..R....L.LLD.N
Retrocopy EDVSSME*LWVKLHFLSLSR*KWWTTTPTPTQEEERQRAGV>TDRYVAR-RGGAGAQSRRVA-LYLLDFN

Parental  DENSNQSFHSEGSLQKGTEPSPGGTPQPSRPVSPAGPPERVTTEEVQPP
          ..NS.QSFHSEGSLQKGTEPSPGGT.QP...VS.AG.PE..TT.....P
Retrocopy NDNSSQSFHSEGSLQKGTEPSPGGTLQPRHSVSLAGLPEAPTTGPRERP

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_517 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 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007604	2 retrocopies	retro_amel_1090, retro_amel_1613,
Bos taurus	ENSBTAG00000008412	1 retrocopy	retro_btau_618,
Canis familiaris	ENSCAFG00000016715	1 retrocopy	retro_cfam_898,
Dipodomys ordii	ENSDORG00000001676	1 retrocopy	retro_dord_517 ,
Equus caballus	ENSECAG00000000482	1 retrocopy	retro_ecab_704,
Felis catus	ENSFCAG00000029090	1 retrocopy	retro_fcat_1969,
Macaca mulatta	ENSMMUG00000003225	13 retrocopies	retro_mmul_1247, retro_mmul_1613, retro_mmul_1818, retro_mmul_2108, retro_mmul_2153, retro_mmul_2644, retro_mmul_390, retro_mmul_724, retro_mmul_740, retro_mmul_750, retro_mmul_755, retro_mmul_791, retro_mmul_975,
Mustela putorius furo	ENSMPUG00000011988	1 retrocopy	retro_mputfur_954,