RetrogeneDB ID: retro_dord_145

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_3792:57924..58924(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hnrpdl
• Ensembl ID: ENSDORG00000000968
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:MGI Symbol;Acc:MGI:1355299]

Sequence

>retro_dord_145
CTCTTCCGCCGCCATTTTAAATCTAGCTCCATACAACGCTCCACCGCTGCCGCCAGCCGGACTACGCGCCACCACCCTCC
GACCGACCATTCCGCCACCATGGAGGACATGAACGAGTACAGCAACATAGAGGAGTTCGCAGAGGGATCCAAAATCAACG
CGAGCAAGAATCAGCAGGATGACGGTAAAATGTTTATTGGAGGCTTGAGCTGGGATACGAGCAAGAAAGATCTGACAGAG
TGTTTGTCTCGATTTGGGGAAGTTGTAGACTGCACAATCAAAACAGATCCAGTCACCGGAAGATCAAGAGGATTTGGGTT
TGTGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTGGATGGCAAATTGATAGATC
CTAAAAGGATCTATCAAAGCCAAAGCTTTGAAAGGCAAAGAACCCCCTAAAAAGGTTTTTGTGGGTGGATTGAGCCCAGA
TACTTCTGAAGAACAAATTAAAGAGTATTTTGGAGCTTTTGGAGACATTGAAAATATTGAACTTCCCATGGATACAAAAA
CAAATGAGAGAAGAAGGTTTTGCTTTATCACATATACAGATGAGGAGCCAGTAAAGAAATTGTTAGAAAGCAGATATCAT
CAAATTGGTTCTGGGAAGTGTGAGATCAAAGTTGCCCAGCCCAAGGACGTGTATAGGCAGCAACAGCAACAACAAAAAGG
AGGAAGAGGTGCTGCAGCTGGAGGAAGAGGTGGTACTAGGGGTCGTGGCCAAAACTGGAACCAAGGATTTAATAGCTATT
ATGATCAAGGATATGGAAATTACAATAGTGCCTATGGTGGTGATCAAAACTATAGTGGCTATGGCGGATATGATTATACT
GGGTATAACTATGGGAACTATGGATATGGACAGGGATATGCAGACTACAGTGGTCAACAGAGCACTTATGGCAAGGCATC
TCGAGGTGGTGGCAATCACCAAAATAATTACCAGCCATAC

Alignment

ORF - retro_dord_145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 79.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFRRHFKSSSIQRSAAAAAASRTTRHHPPTDHSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
          LFRRHFKSSSIQRS...AAASRTTRHHPPTDHSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG
Retrocopy LFRRHFKSSSIQRST--AAASRTTRHHPPTDHSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIGG

Parental  LSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKR--
          LSWDTSKKDLTE.LSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKR..
Retrocopy LSWDTSKKDLTECLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRIY

Parental  -AKALKGKEPPKKVF-VGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKL
          ..........P.K.F.VGGLSPDTSEEQIKEYFGAFG.IENIELPMDTKTNERR.FCFITYTDEEPVKKL
Retrocopy QSQSFERQRTP*KGF>VGGLSPDTSEEQIKEYFGAFGDIENIELPMDTKTNERRRFCFITYTDEEPVKKL

Parental  LESRYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGN
          LESRYHQIGSGKCEIKVAQPK.VYRQQQQQQKGGRGAAAGGRGGTRGRG....QNWNQGFN.YYDQGYGN
Retrocopy LESRYHQIGSGKCEIKVAQPKDVYRQQQQQQKGGRGAAAGGRGGTRGRG----QNWNQGFNSYYDQGYGN

Parental  YNSAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
          YNSAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
Retrocopy YNSAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY

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_145 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 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145 ,
Dipodomys ordii	ENSDORG00000005482	1 retrocopy	retro_dord_489,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys	ENSNLEG00000008636	1 retrocopy	retro_nleu_673,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,