RetrogeneDB ID: retro_dord_363

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_138813:1061..1501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gatad1
• Ensembl ID: ENSDORG00000005895
• Aliases: None
• Description: GATA zinc finger domain containing 1 [Source:MGI Symbol;Acc:MGI:1914460]

Sequence

>retro_dord_363
TTAAAAAATCCCATCAAAGCTCCTGAGTCTGTTTCCACCATCATCACTGCAGAATCAATGTTCTACAAAGGAGTATATTA
CCAAAATGGTGATGATGTTTCTGTGATTGATGATCAACATGGAAAGCTCTACACTGCTCAGATCAGGGGTTTTATCTAGG
ACCAGTATTGAGAGAAGAGTGCAGCACTGACGTAGCTTATTCCCACTCTCTCTAGCCCCACAGATCAGTTTGACCCTGTG
TCTTATATCATATGGCCAGAGGAAGACCTTCCCAGGAAGATGGAATACTTGGAATTTGTTTGTCATGCACCGTCTGAGTA
TTTCAAGTCAAGGTCACCACCATTTCCCACTGTCTCCACCAGACCAGAAAAGGGCTATATATGGACTCATGTTGGACCTA
CTCCTGCAATAATGATTAGGAGACAGTTACCAATCACTTG

Alignment

ORF - retro_dord_363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 56.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKMPIKAPESVSTIITAESIFYKGVYYQIGDVVSVIDEQDGKLYYAQIRGFIQDQYCEKSAALTWLIPTL
          LK.PIKAPESVSTIITAES.FYKGVYYQ.GD.VSVID.Q.GKLY.AQIRGFI.DQY.EKSAALT.LIPTL
Retrocopy LKNPIKAPESVSTIITAESMFYKGVYYQNGDDVSVIDDQHGKLYTAQIRGFI*DQY*EKSAALT*LIPTL

Parental  SSPTDQFDPASYII-PEEDLPRKMEYLEFVCHAPSEYFKSRSSPFPTVPTRPEKGYIWTHVGPTPAITIK
          SSPTDQFDP.SYII.PEEDLPRKMEYLEFVCHAPSEYFKSRS.PFPTV.TRPEKGYIWTHVGPTPAI.I.
Retrocopy SSPTDQFDPVSYIIWPEEDLPRKMEYLEFVCHAPSEYFKSRSPPFPTVSTRPEKGYIWTHVGPTPAIMIR

Parental  -ETVANHL
          .ETV.NHL
Retrocopy <ETVTNHL

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_363 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 4 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000193	2 retrocopies	retro_chof_2074, retro_chof_2604,
Dipodomys ordii	ENSDORG00000005895	10 retrocopies	retro_dord_267, retro_dord_270, retro_dord_300, retro_dord_318, retro_dord_363 , retro_dord_459, retro_dord_463, retro_dord_504, retro_dord_551, retro_dord_566,
Monodelphis domestica	ENSMODG00000010701	1 retrocopy	retro_mdom_877,
Oryctolagus cuniculus	ENSOCUG00000014806	1 retrocopy	retro_ocun_1772,