RetrogeneDB ID: retro_dord_657

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_48800:7264..7958(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kin
• Ensembl ID: ENSDORG00000003732
• Aliases: None
• Description: antigenic determinant of rec-A protein [Source:MGI Symbol;Acc:MGI:96676]

Sequence

>retro_dord_657
AATGGCTTCAAGTGTCATTGTCTGTCTGCATCTCATCAGACACAACTGTTGCTGGCTTCAGAAAATCCTCAACCCTTTAT
GGATTGTTTTTCAGAGGCATTTACAAACGACTTTCTAGAACTTCTCAGGAGGCGCTTGGGTACCAGGAGAGTGCACTACA
GCATCGTCTACAACGAGTATGTCAGGCACCGTGGGCACATCCACATGAATGCCACTCAGTGGGAAACACTGACCGACTTT
ACCAAGTGGCTGGGCAGGGAAGGCTTGTGCAAAGTGGATGAGATGCTGAGAGGCTGGTACATTCAGTTCATAGACAGGGA
CCCAGAGACCATTCGGTGGCCACTGGAGCTAGAGAAGCAGCAGAAGCAGGACCTCAACGATGAAGAAAAATCTACTAAGC
TTATTGAAGAGCAAGTGAGACGAGGTTTGGAAGGGAAAGAGCAGGAGACCCCTGTTTTCTCGGAATTCAGCAGAGAAAAC
GATGAAGAGAAAGTCACATTTCGTCTGAATAAAGGAGCATGCAGTTCAGCAGGAATAGTTTCCAAATCAAATCTCTTGGG
GCTAAGTGTCCTGAAAATATTGGGGAGTGCAGCATCTGTCAAGCGAAAAGCCTCTTCCCAGAGCTCAGTGCTGGCTAAAG
AAAAAGAGGAAAAAGAAATCTGCACTGGATGAAATCAGGGAGATTGAAGAGAAG

Alignment

ORF - retro_dord_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 64.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGFKCHCMS-SHQ-RLLLASXXXXXXXXXXXXEFRNDFLELLRR-FGTKRVHNNIVY-EYISHREHIHMN
          NGFKCHC.S.SHQ..LLLAS.............F.NDFLELLRR..GT.RVH..IVY.EY..HR.HIHMN
Retrocopy NGFKCHCLSASHQTQLLLASENPQPFMDCFSEAFTNDFLELLRRRLGTRRVHYSIVYNEYVRHRGHIHMN

Parental  ATQWETLTDFTKWLGREGLCKVDETPKGWYIQYIDRDPETIRRQLELEKKKKQDLDDEEKTAKFIEEQVR
          ATQWETLTDFTKWLGREGLCKVDE...GWYIQ.IDRDPETIR..LELEK..KQDL.DEEK..K.IEEQVR
Retrocopy ATQWETLTDFTKWLGREGLCKVDEMLRGWYIQFIDRDPETIRWPLELEKQQKQDLNDEEKSTKLIEEQVR

Parental  RGLEGKEQETPVFTELSRENDEEKVTFNLNKGACSSAGTSSKSSSLGPSALKTLGSAASVKRKDSSQSSA
          RGLEGKEQETPVF.E.SRENDEEKVTF.LNKGACSSAG..SKS..LG.S.LK.LGSAASVKRK.SSQSS.
Retrocopy RGLEGKEQETPVFSEFSRENDEEKVTFRLNKGACSSAGIVSKSNLLGLSVLKILGSAASVKRKASSQSSV

Parental  QAKE-KKKKKSALDEIMEIEEE
          .AKE.K.KKKSALDEI.EIEE.
Retrocopy LAKE>KRKKKSALDEIREIEEK

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_657 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281, retro_cpor_818, retro_cpor_987, retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344, retro_dord_657 ,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9,