RetrogeneDB ID: retro_dord_666

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_50096:5775..7052(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDORG00000011533
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zc3h15
• Ensembl ID: ENSDORG00000011664
• Aliases: None
• Description: zinc finger CCCH-type containing 15 [Source:MGI Symbol;Acc:MGI:1919747]

Sequence

>retro_dord_666
ATGCCCCCCAAGAAACAGGCTCAGGCCGGGGGCAGCAAAATGGAGGAACAGAAAAAGAAGGAGAAGATTATCGAAGACAA
AACTTTTGGCTTAAAGATTAAGAAAGGAGCAAAACAACAGAAGTTTATCAAGGCTGTCACTCACCAAGTTAAATTTGGTC
AACAAAATCCACATCAGGTAGCACAGAGTGAAGCTGAAAAGAAATTGAAGAAAGATGATAAGAAGAAAGAATTACAAGAA
CTAAATGAGCTGTTCAAACCTGTTGTTGCTGCTCAAAAATTAAGTAAAGGTGTGGATCCCAAGTCTGTGGTGTGTGCCTT
CTTCAAGCAAGGGCTGTGTACTAAAGGAGATAAATGTAAGTTCTCTCATGACTTGACTTTGGAGAGAAAATGTGAAAAAC
GAAGTATTTACATTGATGCAAGGGATGAAGAACTTGAAAAAGACACAATGGAAAATTGGGATGAGAAAAAGCTGGAAGAA
ATAGTGAACAAGAAGCACGGTGAGGCGGAAAAGAGAAAACCAAAAACTCAAATAGTGTGCAAGCATTTCCTTGAAGCTAT
TGAAAATAACAAGTATGGCTGGTTTTGGGTATGTCCTGGAGGAGGTGATAACTGCATGTATCGTCATGCACTTCCTCCTG
GATTTGTATTGGAAAAGAACAAAAAAAAAAAAGAGGAGAAAGAAGATGAAATTTCATTGGAAGACTTGATTGAAAGAGAG
CGCTCTGCCCTAGGTCCAAATGTTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAGAAAAGGAAAAGACAAGAAAA
GACTGATAAACTTGAACAAGATATGGAAAGAAGAAAAGCAGACTTCACATCAGGGAAGGCACTGGTCATCAGTGGTCGTG
AAGTGTTTGAATTTTGTCCTGAACTTGTCGATGATGATGATGAAGAAGCAGATGACACCGTTACATTCAGGGAACAAGAG
GTGATGAGATTGATGATTTCATGAGAGTAAATGACATAGATTTAAGTCTGTACGTCCCTACAGCTGTAGATGAGACAGGT
ATTACTGTACCCAGTCTTGAAATATTCAACACATTTGCTTTGGATAAAGATGAAAACAAATTAAGTGAAGCATCTGGAGG
TAGGGCAGAAAATGGCGAAAGAAGTGATTTGGAAGAGGACAATGAAGGGGAAGGACAGGAAAATGGAGCCATCGATGCTG
CACCTGTTGATGAAAATCTTTTTACTGGGGAAGATTTGGATGAATTAGAAGAAGAATTAAACACACTTGATTTAGAA

Alignment

ORF - retro_dord_666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.27 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
          MPPKKQAQAGGSK..EQKKKEKIIEDKTFGLK.KKGAKQQKFIKAVTHQVKFGQQNP.QVAQSEAEKKLK
Retrocopy MPPKKQAQAGGSKMEEQKKKEKIIEDKTFGLKIKKGAKQQKFIKAVTHQVKFGQQNPHQVAQSEAEKKLK

Parental  KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA
          KDDKKKELQELNELFKPVVAAQK.SKG.DPKSVVCAFFKQG.CTKGDKCKFSHDLTLERKCEKRS.YIDA
Retrocopy KDDKKKELQELNELFKPVVAAQKLSKGVDPKSVVCAFFKQGLCTKGDKCKFSHDLTLERKCEKRSIYIDA

Parental  RDEELEKDTMENWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGW-WVCPGGGDNCMYRHA
          RDEELEKDTMENWDEKKLEE.VNKKHGEAEK.KPKTQIVCKHFLEAIENNKYGW.WVCPGGGDNCMYRHA
Retrocopy RDEELEKDTMENWDEKKLEEIVNKKHGEAEKRKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDNCMYRHA

Parental  LPPGFVLKKD--KKEEKEDEISLEDVIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKA
          LPPGFVL.K.....EEKEDEISLED.IERERSALGPNVTKITLESFLAWKKRKRQEK.DKLEQDMERRKA
Retrocopy LPPGFVLEKNXXXXEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKTDKLEQDMERRKA

Parental  DFKAGKALVISGREVFEFRPELVNDDDEEADDT-RYIQGTGGDEVDDSMSVNDIDLSLYVPRAVDETGIT
          DF..GKALVISGREVFEF.PELV.DDDEEADDT.RYIQGT.GDE.DD.M.VNDIDLSLYVP.AVDETGIT
Retrocopy DFTSGKALVISGREVFEFCPELVDDDDEEADDT<RYIQGTRGDEIDDFMRVNDIDLSLYVPTAVDETGIT

Parental  VASLERFNTYALDKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDELEEE
          V.SLE.FNT.ALDKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDA.PVDENLFTGEDLDELEEE
Retrocopy VPSLEIFNTFALDKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAAPVDENLFTGEDLDELEEE

Parental  LNTLDLE
          LNTLDLE
Retrocopy LNTLDLE

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_666 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666 ,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,