RetrogeneDB ID: retro_dord_400

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_16531:329..1472(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000002605
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Glud1
• Ensembl ID: ENSDORG00000009767
• Aliases: None
• Description: glutamate dehydrogenase 1 [Source:MGI Symbol;Acc:MGI:95753]

Sequence

>retro_dord_400
GTCCCCTTTGGGGGGGCCAAAGCTGGCGTGAAGATCAATCCCAAAAACTATTCTGACAATGAGCTGGAAAAGATCACCAG
GAGGTTTGCCATGGAACTAGCCAAAAAAGGCTTCATTGGTCCCAGCGTTGATGTGCCTTCTCCAGACATGGGCACAAGTG
AGCGGGAAATGGCCTGGATCGCTGACACCTATGCCACCACCATAGGACATTTTGATATTAATGCCCGCGCCTGCGTTACT
GGGAAACCCATTAGTCAGGGTGGTATTCGTGGCCGGATCTCTGCTACGGGTCGTGGTGTTTACTATGGAATAGAAAACTT
CCTCAATGAAGTTCCCTACATGAATACTGTAGGACTGACCCCGGGGCTTAAAGACAAAACGTTTGTTATTCAGGGATTTG
GTAATGTGGGCCGGTACGCTATGAAATACTTGCATGGTTCTGGGGCTAAATGTGTTGGTGTTGGTGAATATAATGGCAGC
ATATGGAATTCAGACGGCATAGATCCAAAGGACCTGGAAGAGTTCAAATCGCAACATGGAACAATCCTGGGTTTCCCCCA
GGCAAAACTCTATGAGGGAAACATTTTAGAAGCAGACTGTGATATTTTGATCCCTGCTGCCATGGAAAAGCAGTTGACCA
AATCTGTTGCATCCAGAGTCAAAGCCAAGATCATAGCTGAAGCTGCCAATGGACCAACAACTCCAGAAGCTGATAAAATT
TTTCTAAAGAGAAACATTCTGGTTATTCCTGATCTCTATTTGAATGCTGGTGGAGTGACAGTATCTTATTTTGAGTGGCT
GAAGAATATAAGTCATGTCAGCTATGGACGTTTGACCTTCAAATATGAAAGAGATGCTAACTACCAGTTGCTCATGTCTG
TTCAAGAAAGTTTAGAAAAAAAGTTTGGGAAGCATCCTGGAACTATTCCTGTTGTACCCACAGCAAGGCTCCAAAGCAGA
ATAAAAGCTGCATCTGAGAAAGACATTGTATATTCTGGTTTAGCTCACACTATGGAAAAATCTGCCAAGCAAATCATAAA
CACAGCCACTAAGTATAACCTGGGATTAGATTTAAGAACGGCAGCCTATATCAATGCCATTGTGAAAGTCTTCAAGGTAT
ACCAAGAAGCTGGTTTGACCTTC

Alignment

ORF - retro_dord_400 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.15 %
• Parental protein coverage: 68.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGH
          VPFGGAKAGVKINPKNY.DNELEKITRRF.MELAKKGFIGP..DVP.PDM.T.EREM.WIADTYA.TIGH
Retrocopy VPFGGAKAGVKINPKNYSDNELEKITRRFAMELAKKGFIGPSVDVPSPDMGTSEREMAWIADTYATTIGH

Parental  YDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHS
          .DINA.ACVTGKPISQGGI.GRISATGRGV..GIENF.NE..YM...G.TPG..DKTFV.QGFGNVG...
Retrocopy FDINARACVTGKPISQGGIRGRISATGRGVYYGIENFLNEVPYMNTVGLTPGLKDKTFVIQGFGNVGRYA

Parental  MRYLHRFGAKCVGVGESDGSIWNPDGIDPKELEDFKLQHGSILGFPKAKVYEGSILEADCDILIPAASEK
          M.YLH..GAKCVGVGE..GSIWN.DGIDPK.LE.FK.QHG.ILGFP.AK.YEG.ILEADCDILIPAA.EK
Retrocopy MKYLHGSGAKCVGVGEYNGSIWNSDGIDPKDLEEFKSQHGTILGFPQAKLYEGNILEADCDILIPAAMEK

Parental  QLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTF
          QLTKS.A.RVKAKIIAE.ANGPTTPEADKIFL.RNI.VIPDLYLNAGGVTVSYFEWLKN..HVSYGRLTF
Retrocopy QLTKSVASRVKAKIIAEAANGPTTPEADKIFLKRNILVIPDLYLNAGGVTVSYFEWLKNISHVSYGRLTF

Parental  KYERDSNYHLLMSVQESLERKFGKHGGTIPVVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAM
          KYERD.NY.LLMSVQESLE.KFGKH.GTIPVVPTA..Q.RI..ASEKDIV.SGLA.TME.SA.QI..TA.
Retrocopy KYERDANYQLLMSVQESLEKKFGKHPGTIPVVPTARLQSRIKAASEKDIVYSGLAHTMEKSAKQIINTAT

Parental  KYNLGLDLRTAAYVNAIEKVFKVYNEAGVTF
          KYNLGLDLRTAAY.NAI.KVFKVY.EAG.TF
Retrocopy KYNLGLDLRTAAYINAIVKVFKVYQEAGLTF

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_400 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 20 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007540	2 retrocopies	retro_btau_1413, retro_btau_1741,
Canis familiaris	ENSCAFG00000016095	1 retrocopy	retro_cfam_747,
Choloepus hoffmanni	ENSCHOG00000001101	1 retrocopy	retro_chof_2002,
Callithrix jacchus	ENSCJAG00000011633	1 retrocopy	retro_cjac_2830,
Dipodomys ordii	ENSDORG00000009767	1 retrocopy	retro_dord_400 ,
Equus caballus	ENSECAG00000007371	2 retrocopies	retro_ecab_886, retro_ecab_919,
Echinops telfairi	ENSETEG00000019638	2 retrocopies	retro_etel_141, retro_etel_2024,
Homo sapiens	ENSG00000148672	1 retrocopy	retro_hsap_31,
Gorilla gorilla	ENSGGOG00000015770	1 retrocopy	retro_ggor_2954,
Loxodonta africana	ENSLAFG00000012059	1 retrocopy	retro_lafr_504,
Microcebus murinus	ENSMICG00000016526	1 retrocopy	retro_mmur_524,
Monodelphis domestica	ENSMODG00000002756	1 retrocopy	retro_mdom_124,
Nomascus leucogenys	ENSNLEG00000011658	1 retrocopy	retro_nleu_36,
Otolemur garnettii	ENSOGAG00000003641	1 retrocopy	retro_ogar_2757,
Procavia capensis	ENSPCAG00000008662	1 retrocopy	retro_pcap_11,
Pongo abelii	ENSPPYG00000002827	3 retrocopies	retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes	ENSPTRG00000002711	4 retrocopies	retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus	ENSSTOG00000012843	1 retrocopy	retro_itri_737,
Tarsius syrichta	ENSTSYG00000001578	1 retrocopy	retro_tsyr_313,
Tursiops truncatus	ENSTTRG00000008145	1 retrocopy	retro_ttru_950,