RetrogeneDB ID: retro_dord_28

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_22459:25467..26244(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000012172
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000014818
• Aliases: None
• Description: None

Sequence

>retro_dord_28
TGCAGGAAAATGGCATCACTCTCTTTCCTTAATCGACCCGGCCTTCCAAACCTGGCGTACAAGAGTTTAAAAGGCAAAAC
ACCGGGAATTATCTTCATCCCTGGTTATCTTTCTACTATGAATGGTACAAAAGCATTGGCCATTGAGGAATTTTGCAAAT
CTGTAGGTCACGCCTATATAAGGTTTGACTATTCAGGAGTTGGAAATTCAGATGGTAACTTAAAAGATTGCACTGTGGGG
AAATGGAGAAAAGATGTGCTTTCTATACTTGATGATATAGCCAAAGGACCGCAGATTCTAATTGGTTCTAGTCTTGGTGG
ATGGCTTATGCTTCATGCTGCAGTTGCACGGCCAGAAAAGGTTGTGGCTCTTATTGGTGTAGCTACAGCTACAGATGCTC
TAGTGACACAGTTCCGTCAGCTTCCTGTTGAGGTACAAAAGGAAGTTGAGATGAAAGGTGTTTGGTCCATGCCATCAAAA
TACACTGAGGAAGGATATCATCACATTCAGTACAGTTTCATTAAGGAAGCAGAGCACCATTGCTTGTTACACAGCCCTAT
TTCCGTGCACTGTCCTGTAAGATTGCTCCATGGCATGATGGATGACGTAATCCCTTGGCATACGTCCATGCAGGTTGCTG
ACCGACTACTTAGCACAGATGTCGATGTCATCCTCAGGAAACACAGTGATCATGAAATGAAGGAAAAGGCAGACATTCAA
CTTCTTGTGTACACGATTGACGATTTAATTGAGAAGCTCTCATCCATGCCACAATAG

Alignment

ORF - retro_dord_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FDRSGVGNSDGNQKDSTRGKRRKDVLSIRDDIAKGPQILIGSSLGGWLMLHAAVARPEKVVALIGVATAT
          FD.SGVGNSDGN.KD.T.GK.RKDVLSI.DDIAKGPQILIGSSLGGWLMLHAAVARPEKVVALIGVATAT
Retrocopy FDYSGVGNSDGNLKDCTVGKWRKDVLSILDDIAKGPQILIGSSLGGWLMLHAAVARPEKVVALIGVATAT

Parental  DALVTQFRQLPVESKEE--MKGV-VMPSKYTEEGYHHIQYSS-KEAEHHCLLHSPIPVHCPVRLLHGMMD
          DALVTQFRQLPVE...E..MKGV..MPSKYTEEGYHHIQYS..KEAEHHCLLHSPI.VHCPVRLLHGMMD
Retrocopy DALVTQFRQLPVEVQKEVEMKGVWSMPSKYTEEGYHHIQYSFIKEAEHHCLLHSPISVHCPVRLLHGMMD

Parental  DVIPWHTSMQVADRLLSTDVDVILRKHSDHEMKEKADIQLLVYTIDDLIEKLSSMPQ
          DVIPWHTSMQVADRLLSTDVDVILRKHSDHEMKEKADIQLLVYTIDDLIEKLSSMPQ
Retrocopy DVIPWHTSMQVADRLLSTDVDVILRKHSDHEMKEKADIQLLVYTIDDLIEKLSSMPQ

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_28 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020230	1 retrocopy	retro_cjac_2973,
Cavia porcellus	ENSCPOG00000005650	1 retrocopy	retro_cpor_1498,
Dipodomys ordii	ENSDORG00000014818	1 retrocopy	retro_dord_28 ,
Felis catus	ENSFCAG00000029739	1 retrocopy	retro_fcat_176,
Ochotona princeps	ENSOPRG00000009517	1 retrocopy	retro_opri_1051,
Tursiops truncatus	ENSTTRG00000016358	1 retrocopy	retro_ttru_778,