RetrogeneDB ID: retro_dord_184

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_4835:25507..26110(-)
• Located in intron of: ENSDORG00000010015

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ghitm
• Ensembl ID: ENSDORG00000001109
• Aliases: None
• Description: growth hormone inducible transmembrane protein [Source:MGI Symbol;Acc:MGI:1913342]

Sequence

>retro_dord_184
ATAATCTGGCCTCAGTATGTGATGGATAGAAAACATTCTACCTGTATGTACTTAGCATAAAGTATTGGTGTAACAGCTTT
GTCTGCTTTGGCAATAGCCAGATCTCCTGTTCTCATGAATCTCATGCTGAGAGGCTCTTGGGTGACAACTGGCGCAACCA
TTGCAGCCATGATTGGAGCTGGAATGCTAGTACAGTCCATATCCCATCACCAGAACAAGGGCCCGCAGCATCTTGCTTGG
TTGCTACATTCTGGTGTGATGGCTCCTCTGACAATACTAGGGGGACCCCTTCTCATAAGAACTGCATGGTACACTACCGG
CATTGTAGGAGGCCTCTCCACTGTGGCCATGTATGCTCCCAGAGAGAAGTTTTTGAACATGGGTGTCCTACTGGGAGTGG
GCCTAGGTCTTGTATTTGTGTCTTCACTGGGGTCCATGTTTCTGCCACAGAACACTGTGGCTGGTGCCATCCTGTACTCA
GTGGCAATGTATGGTAGATTAGTTATTTTCAGTATGTTCCTTCTATATGATACTCAGAAAGTAATCAAATGTGCAATTGT
ATGGACAGAACAGATATGAGACAATCAATTTGATGTTGTGAAT

Alignment

ORF - retro_dord_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 67.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIWPQYVKDRIHSTYMYLAGSIGVTALSALAIAKSPVLMNFMLRGSWVTVGATLVAMIGAGMLVQSISYH
          .IWPQYV.DR.HST.MYLA.SIGVTALSALAIA.SPVLMN.MLRGSWVT.GAT..AMIGAGMLVQSIS.H
Retrocopy IIWPQYVMDRKHSTCMYLA*SIGVTALSALAIARSPVLMNLMLRGSWVTTGATIAAMIGAGMLVQSISHH

Parental  QNKGPKHLAWLLHSGVMGAVVAPLTILGGPLLIRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLGVGLG
          QNKGP.HLAWLLHSGVM....APLTILGGPLLIR.AWYT.GIVGGLSTVAM.AP.EKFLNMG..LGVGLG
Retrocopy QNKGPQHLAWLLHSGVM----APLTILGGPLLIRTAWYTTGIVGGLSTVAMYAPREKFLNMGVLLGVGLG

Parental  LVFVSSLGSMFLAPNTVAGATLYSVAMYGGLVLFSMFLLYDTQKVVKRA-EGTPLYGQNRYDPIN
          LVFVSSLGSMFL..NTVAGA.LYSVAMYG.LV.FSMFLLYDTQKV.K.A...T.....N..D..N
Retrocopy LVFVSSLGSMFLPQNTVAGAILYSVAMYGRLVIFSMFLLYDTQKVIKCAIVWTEQI*DNQFDVVN

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_184 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184 ,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,