RetrogeneDB ID: retro_dord_474

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_21422:15491..16130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kansl2
• Ensembl ID: ENSDORG00000001180
• Aliases: None
• Description: KAT8 regulatory NSL complex subunit 2 [Source:MGI Symbol;Acc:MGI:1916862]

Sequence

>retro_dord_474
AAGCTGAAGGAGCACAGAATGCTGGCCACTGATGGTGCCTCCCAGCAGGCTCATACCACGCGTTCCAGTCAGAGGTGCTT
GGCCTTTGTGGATGATGTTCGTTGCTCCAATCAGTCTCTTCCAATGACCAAACAATGCCTTACCCATGTTTGTCAGGACA
CAAATCAGGTTCTCTTCAAATGCTGCCAGGGATCTGAAGAGATGCTTTGCCACATGCCAGTTCCTGTAAGCCTCTCTGAG
GATCCCTGCTAACCAGAGCATTCCAGTTGCCTCCTCAGATATATAAGTCCCAGCAAGAACTGTCCGTGCCACACGATCTG
GAAGCCGGCTCCATGGATCTGGACTTGAGTGCTGCTGAGCTTCAGCCCACTGAGAGTTTACCACTGGAGTTCAGTGACGA
TTTCGATGTGTTTGGAGATGGTATGCACTGTCCATCACCTCTGCTTTGGTTTGGTTCCTACATTAACCCTGGAAGATCAT
TCAATCAAAGAAATTGCTGAAGGTTCGGTGGATATTTTAGGCCAAATGCCAGTGGCTGGAGATGGGTGCAGATCCCAGGG
ATCTCGAAATTCTGAGAAAGCTTGTGCGCTACTGCCTCAAAGTGGATCGGCTACTGCCAATGGGAAACCAGAACCCACT

Alignment

ORF - retro_dord_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 68.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLKERRMLATDGASQQAHTTRSSQRCLAFVDDVRCSNQSLPMTRHCLTHICQDTNQVLFKCCQGSEEVPC
          .LKE.RMLATDGASQQAHTTRSSQRCLAFVDDVRCSNQSLPMT..CLTH.CQDTNQVLFKCCQGSEE..C
Retrocopy KLKEHRMLATDGASQQAHTTRSSQRCLAFVDDVRCSNQSLPMTKQCLTHVCQDTNQVLFKCCQGSEEMLC

Parental  NKPVPVSLSEDPCCPLH-FQLPPQMYKPQQVLSVPHDLEAGPMDLYLSAAELQPTESLPLEFSDDLDVVG
          ..PVPVSLSEDPC.P.H.FQLPPQ.YK.QQ.LSVPHDLEAG.MDL.LSAAELQPTESLPLEFSDD.DV.G
Retrocopy HMPVPVSLSEDPC*PEH<FQLPPQIYKSQQELSVPHDLEAGSMDLDLSAAELQPTESLPLEFSDDFDVFG

Parental  DGMQCPPSPLLFD-PSLTLEDHSIKEIAEGSVDILGQIPVAGDGCRSQGSRNSEKACALLPQSGLATANG
          DGM.CP...L.F..P.LTLEDHSIKEIAEGSVDILGQ.PVAGDGCRSQGSRNSEKACALLPQSG.ATANG
Retrocopy DGMHCPSPLLWFG>PTLTLEDHSIKEIAEGSVDILGQMPVAGDGCRSQGSRNSEKACALLPQSGSATANG

Parental  KPEPT
          KPEPT
Retrocopy KPEPT

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_474 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005760	1 retrocopy	retro_cpor_1491,
Dipodomys ordii	ENSDORG00000001180	1 retrocopy	retro_dord_474 ,
Mus musculus	ENSMUSG00000022992	2 retrocopies	retro_mmus_2944, retro_mmus_3134,
Rattus norvegicus	ENSRNOG00000010904	3 retrocopies	retro_rnor_1071, retro_rnor_2831, retro_rnor_792,
Tupaia belangeri	ENSTBEG00000016536	1 retrocopy	retro_tbel_1374,