RetrogeneDB ID: retro_dord_482

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22488:11449..12049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Alg14
• Ensembl ID: ENSDORG00000008564
• Aliases: None
• Description: asparagine-linked glycosylation 14 [Source:MGI Symbol;Acc:MGI:1914039]

Sequence

>retro_dord_482
ATTTTCAAAGCCTGTATAGGAACTGTGGTGGTCATCCTCAGCCTGAGACTATGGGTAGTACTTTGGACCTAGGAGGTTAT
TCCTTGGGAGTGTCTCAGTCTCTTGGTAGTGGCTGGTTCTGGTGGAAATACCACAGAGATCCTGAGGCTAGTTGGAAGCT
TGTGCAATGCTTATTCGCCTAAACATTGTATCATTGCTTATACCAGTAAAATGAGTGCCAGTGAAATTAATTCTTTTGAA
CTTGATCATGCTGGAAGAGAACCTAGTACCATGGACACCAAATGCCACATCCCCAAATTCCGAGAAGCCAGCAGTCCTGA
CTGTCCACAGTGCTCACCACCATCTGGGCCTCTGTGGCTCTCCTTTGCTATGATTTTCCAGATAAAGCCAGATTTGGTGT
TGTGTAACGAACCAAGAACATATGTTCCTATCTTTGTATCTGCCCTCCTCCTTGGCATCCTTGGAATAAAGAAGGTGATC
ATTGTCTTCATTGAGAGCAACTGCGGAGTGGAAACATTATCCCTGTCCGGAAAGATTCTGTTCCATCTCCGGGATTACTT
CATTGTTCATTGGCCAGCTCTAAAGGGGAAGTATCCCAAA

Alignment

ORF - retro_dord_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.17 %
• Parental protein coverage: 94.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILAVAIGAVAVVLGLRLWIVLRTKEVIPRECFSLLVVAGSGGHTMEILRLVGSLSNAYSPRHYIIADTDK
          I....IG.V.V.L.LRLW.VL.T.EVIP.EC.SLLVVAGSGG.T.EILRLVGSL.NAYSP.H.IIA.T.K
Retrocopy IFKACIGTVVVILSLRLWVVLWT*EVIPWECLSLLVVAGSGGNTTEILRLVGSLCNAYSPKHCIIAYTSK

Parental  MSASKIKSFESDRAEREPSTMYTEYHIH-QIPRSREVQQSWLSTVLTTTWA-IWFSFPTVFRIKPDLVLC
          MSAS.I.SFE.D.A.REPSTM.T..HI..QIPRS...QQS.LSTVLTT.WA..W.SF...F.IKPDLVLC
Retrocopy MSASEINSFELDHAGREPSTMDTKCHIP<QIPRS---QQS*LSTVLTTIWA>LWLSFAMIFQIKPDLVLC

Parental  NGPGTCVPICVSAFFLGILGIKKVIIVYVESICRVETLSLSGKILFHLSDYFIVQWPALKEKYPK
          N.P.T.VPI.VSA..LGILGIKKVIIV..ES.C.VETLSLSGKILFHL.DYFIV.WPALK.KYPK
Retrocopy NEPRTYVPIFVSALLLGILGIKKVIIVFIESNCGVETLSLSGKILFHLRDYFIVHWPALKGKYPK

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_482 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000008564	1 retrocopy	retro_dord_482 ,
Procavia capensis	ENSPCAG00000014267	1 retrocopy	retro_pcap_280,
Ictidomys tridecemlineatus	ENSSTOG00000025476	1 retrocopy	retro_itri_1820,
Tursiops truncatus	ENSTTRG00000016557	1 retrocopy	retro_ttru_88,