RetrogeneDB ID: retro_dord_596

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_3808:79644..80051(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm12
• Ensembl ID: ENSDORG00000016381
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1919592]

Sequence

>retro_dord_596
TCCAGTGGAAAGCCCGACCACGCAGACATCTTGCTCATAAACTTACAGCATGTTTCAGAAGTGGAAATAATGGATGACTG
AACAGAAACCCCTCCTCCCCTAGCTTCACTCAATGTTAGTAAGCTTGCCAGCAAAGCGTGGACAGAGAAGAAGGAGAAGC
TGAGCCAGACCTGTGCGATCAGCGCTGGTGTCTTCCTAGAGGGCCAGCAGTAATTCCAGACCATTCACAAGACCATTAAA
GACTGTAAATGGCAAGAAAAAAAAACATTGAGGTCATGGAAGAAATTGTAATTACACCTCCATATCAAGTGGAAAACGGT
AAAGGCAGAGAAGGGAGTGCACTGAGCCATGTATGCAAGATAGTTGAAAAACATTGTAGAGATGTGGAAAGCCAATAGAT
ACTGCAG

Alignment

ORF - retro_dord_596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 88.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQ
          SSGKP.HADILLINLQ.VSEVEI..D.TETPPPLASLNVSKLASKA.TEK.EKLSQ..AISAGV.LEGQQ
Retrocopy SSGKPDHADILLINLQHVSEVEIMDD*TETPPPLASLNVSKLASKAWTEKKEKLSQTCAISAGVFLEGQQ

Parental  LFQTIHKTIKDCKWQ-EKNIVVMEEVVITPP-YQVENCKGKEGSALSHVRKIVEKHFRDVESQKILQ
          .FQTIHKTIKDCKWQ.........E.....P.YQVEN.KG.EGSALSHV.KIVEKH.RDVESQ.ILQ
Retrocopy *FQTIHKTIKDCKWQ<XXXXIEVMEEIVITPPYQVENGKGREGSALSHVCKIVEKHCRDVESQ*ILQ

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_596 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001198	1 retrocopy	retro_chof_1429,
Dipodomys ordii	ENSDORG00000016381	1 retrocopy	retro_dord_596 ,
Erinaceus europaeus	ENSEEUG00000002419	1 retrocopy	retro_eeur_603,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Myotis lucifugus	ENSMLUG00000006391	1 retrocopy	retro_mluc_2205,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Pteropus vampyrus	ENSPVAG00000013706	1 retrocopy	retro_pvam_172,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,