RetrogeneDB ID: retro_dord_742

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_70307:3669..4412(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000008216
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pcbp3
• Ensembl ID: ENSDORG00000003640
• Aliases: None
• Description: poly(rC) binding protein 3 [Source:MGI Symbol;Acc:MGI:1890470]

Sequence

>retro_dord_742
ATGGACGCCGGTGTGACCGAAAGCGGACTAATGTGACTCTCCACCATTCGGCTGCTATGCACGGGAAGGAAGTGGGGAGC
ATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATTG
TCCGGAGAGAATCATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCCTTCGCCATGATCATCGACAAGCTGGAGG
AAGATATCAACAGCTCCATGACCAACAGCACGGCGGCCAGCAGGCCCCCGGTCACCCTGAGGCTGGTGGTGCCGGCCACC
CAGTGCGGCTCCCTGATTGGGAAAGGCGGCTGTAAGATCAAAGAGATCCGCGAGAGCACAGGGGCCCAGGTCCAGGTGGC
GGGGGATATGCTGCCCAACTCCACCGAGCGGGCCATTACCATCGCTGGTGTACCGCAGTCTGTCACCGAGTGTGTCAAGC
AGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGGAGAGTCATGACCATTCCGTACCAGCCCATGCCG
GCCAGCTCTCCCGTCATCTGCGCGGGCGGCCAAGATCGGTGCAGCGACGCCGCGGGCTACCCCCACGCCACCCATGACCT
GGAGGGACCACCTCTAGATGCCTACTCCATTCAAGGACAACACACCATTTCGCCGCTCGATCTGGCCAAGCTGAACCAGG
TGGCAAGACAACAGTCGCACTTT

Alignment

ORF - retro_dord_742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.2 %
• Parental protein coverage: 67.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MESKVSEGGLNVTLTIRLL-MHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIF
          M...V.E.GL....TIRLL.MHGKEVGSIIGKKGE.VK..REESGARINISEGNCPERI.T.TGPT.AIF
Retrocopy MDAGVTESGLM*LSTIRLL<MHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIF

Parental  KAFAMIAYKFEEDIINSMSNSLATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLP
          KAFAMI..K.EEDI..SM.NS.A.S.PPVTLRLVVPA.QCGSLIGKGG.KIKEIRESTGAQVQVAGDMLP
Retrocopy KAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLP

Parental  NSTERAVTISGTPDAIIQCVKQICVVMLES---PPKG--ATIPYRPKPASTPVIFAGGQVRADPLAASTA
          NSTERA.TI.G.P.....CVKQIC.VMLE.....P.G...TIPY.P.PAS.PVI.AGGQ.R....AA...
Retrocopy NSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCSD-AAGYP

Parental  NLSLLLQHPPLPAYTIQGQYAIPHPDLTKLHQLAMQQTPF
          .....L..PPL.AY.IQGQ..I...DL.KL.Q.A.QQ..F
Retrocopy HATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHF

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_742 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742 , retro_dord_748,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095,