RetrogeneDB ID: retro_dord_748

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_7344:29924..30509(+)
• Located in intron of: None

Retrocopy information

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

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_748
ATGGACACCCGTGAGATGGAAGGTGGATTAAATGTCATTCTCACCATCAGGCTACTTATGTATGGAAAGGAAGTTGGCAG
TATCATCGGAAAGAAAGGAGAATCCGTTAAGAAGATTAGAGAGGCGAGTGGTGCACGAATCAACATCTCAGAAGGGAATT
GTCCTGAGAGAATTATCACCTTGGTTGGACCCACTAATGCCATCTTTAAAGCTTTTGCCATGATCATTGACAAACCAGAA
AAAGACGTCGGCAGGTGTATGAACAACACTACAGCTACCAGTAGACCTTTGATCACTCTAAGGTTGGTGATTCCTGCTAG
TCAATGTGGCTCTCTCATTGGAAAAGGTGGTTGCAAGATCAGGCAAATACGAGAAAGTACAGGGGCTCAGATCCAAATGG
CAGCAGACATGCTTCCCAACTCAACTGAGAGGGCCATCAGTATTGCTGGCATACCACAATCCATCATTGAGTGTGTCAAA
CAGATCTGCATGGTCATGTTGGAGTCTCCTCCAAAGGGCATCACCATTCCTTACCGGCCCAAGCCGTCAAGTTCTCTAGC
CAGCTTTGTAGGCGGTCAGGACAGG

Alignment

ORF - retro_dord_748 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 54.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESKVSEGGLNVTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIFK
          M.....EGGLNV.LTIRLLM.GKEVGSIIGKKGE.VKK.RE.SGARINISEGNCPERI.T..GPT.AIFK
Retrocopy MDTREMEGGLNVILTIRLLMYGKEVGSIIGKKGESVKKIREASGARINISEGNCPERIITLVGPTNAIFK

Parental  AFAMIAYKFEEDIINSMSNSLATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPN
          AFAMI..K.E.D....M.N..ATS.P..TLRLV.PASQCGSLIGKGG.KI..IRESTGAQ.Q.A.DMLPN
Retrocopy AFAMIIDKPEKDVGRCMNNTTATSRPLITLRLVIPASQCGSLIGKGGCKIRQIRESTGAQIQMAADMLPN

Parental  STERAVTISGTPDAIIQCVKQICVVMLESPPKGATIPYRPKPASTPVIFAGGQVR
          STERA..I.G.P..II.CVKQIC.VMLESPPKG.TIPYRPKP.S....F.GGQ.R
Retrocopy STERAISIAGIPQSIIECVKQICMVMLESPPKGITIPYRPKPSSSLASFVGGQDR

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_748 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,