RetrogeneDB ID: retro_dord_381

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_14970:3601..4191(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam49b
• Ensembl ID: ENSDORG00000005160
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:MGI Symbol;Acc:MGI:1923520]

Sequence

>retro_dord_381
GAGCAGGCTTTTGCTAAACAGTTTGCCTAAATTCTTCATTTCACATCCCAGTTTGATGAACTGACAAATAACAAATCTTG
CCATACAGAATTCAGATGCTCTAAAAGCAGAGTAAATTGTATAGTAATTAATAATGTTCCTATAGGAGACAAAAGAAATA
ATGAATTGGCAAACTGAATGTCATTTTTTATATATTGAGGTGACCCCCAATGTTGGAAACTAAGTGAAGTGATGACAAAA
TTTCTATCAGAGAATGAAAATTCACCAATAGACAATATCACAGATAGTTTCAGCACCATGGCTAGTGCATGCACAGTATT
GCTGAAAACACTGGAATCCAAATGCAGATTTACAAAGGAAGAGAAAATGTCATTCTACTTGAGGGAAATGGTGTGTGTCA
ACATACTCTATGACCATCACACCTGGTGAGGAGCATTTGAAAAACTTAAAATATTGATATGAAAGGTAGATTTATAGTTT
TTAATGACCAACTTCCATATAATGCAGAAGGTTGTTGAAATACTTTCAGGTACATTCTAAAACATTTGAGTCATGAGACC
ACGTCCAATCAAGTTAAATCCTTGCTGCAA

Alignment

ORF - retro_dord_381 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.74 %
• Parental protein coverage: 61.61 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQALAKQFAEILHFTLRFDELKMTNPAIQNDFSYYRRTLSRMRINNVPAEGENEVNNELANRMSLFYAEA
          EQA.AKQFA.ILHFT..FDEL...N......F...........INNVP.......NNELAN.MS.F....
Retrocopy EQAFAKQFA*ILHFTSQFDELT-NNKSCHTEFRCSKSRVNCIVINNVPIGDKR--NNELAN*MSFFIY*G

Parental  TPMLKTLSDATTKFVSENKNL-IENTTDCLSTMASVCRVMLETPEYRSRFTNEETVSFCLRVMVGVIILY
          .P....LS...TKF.SEN.N..I.N.TD..STMAS.C.V.L.T.E...RFT.EE..SF.LR.MV.V.ILY
Retrocopy DPQCWKLSEVMTKFLSENENSPIDNITDSFSTMASACTVLLKTLESKCRFTKEEKMSFYLREMVCVNILY

Parental  DH-VHPVGAFAKTSKIDMKGCIKVLKDQPPNSVEGLLNALRYTTKHLNDETTSKQIKSMLQ
          DH..H.V....KT..IDMKG...V..DQ.P...EG..N..RY..KHL..ETTS.Q.KS.LQ
Retrocopy DH<SHLVRSI*KT*NIDMKGRFIVFNDQLPYNAEGC*NTFRYILKHLSHETTSNQVKSLLQ

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_381 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381 ,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978,