RetrogeneDB ID: retro_dord_231

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: GeneScaffold_6180:515565..516826(-)
• Located in intron of: ENSDORG00000003291

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDORG00000013324
• Aliases: None
• Description: None

Sequence

>retro_dord_231
ATGAGCATCAGGACGCCACCCACACTGCAGCATCTAGCCCTGCAAAGCCTACTGAGCAAAGAGTCCCAGGCCATCTCGGT
CCTGGAGGATCTGCCGGTGCTGCTGTTCCCCCCACTCTTCATGGAGGTCTACGCACAGGGCCGCACAGAGGTGCTGAAGG
CCATGGTGCAGGCCTGGCCCTTCCCCTGCCTTCCCCTGGGGGACCTGGCAGAGTCCCCAGACCTGGAGACCTTCAAAGCT
GTCCTGGATGGGCTTGATCTGCTGCTACTTGCCAAGAAGGAGCGCCCCAGGCGGTGGAAACTGCAAGTAGTCGATCTGCG
GAAAGCACACCCTGAGATCTGGATACGGGGATACCCCTCCATGGCGCAAATCTCCTCTCCACATGTTCCTGACTGAAAGG
CCAACAGACAGTCGCCTTTCAGCTGGGACTGAAGAGCAGCCCTTGATCCTCGCCATTGACCTGACCGTCAGAGATGGCAC
CCAGGATGCTTTCCAAGCCTACCTCCTCCAGTGGGCCAGGAAGAGGAAAGGACGAGTCCAGCTGTGCTCAACCAAGCTGC
AGATTCTGTCTGGCTCCATCTACAAAATCCAGAAGGCTCTGCATGCCGTGCGCCTGGACTCCATCCAGGAACTGGTGGTG
AACAATTTCTGGCATCGAGAAACCATGAGAAAATTCGCTCCTTCCCTGGACCAGATGAGGAACCTTTGCCTGCTCACCTT
CTCCAAGATGAGTGTCGACTTCTACACTTCCAGCCGCCGGAATCTCTGGTATTCCCGCAAATATGCGGCGCATCTGGGGC
AGCTGCAGCATCTCCAGGAGCTTCGTGTGCACGATGTCTTCTTCCTGTATGGACGGCTGCCCGCCATCCTCAGCAGCCTG
ACGCCTTTGAACACCTTGTCTTTGAGCTCATGTCCACTGAAGGAAGCCGACCTGAGGTTTTTGTGCCAGTGTCCCTGCAC
CAGGCAGCTCAAGCACCTGCGTCTGAGGAGTTTGTGCATGGGCCGCTTCAGTCCTGAGCCCCTGCGAGCCCTGCTGGAGC
AAGTGGCCGGCACCCTGGAGACCCTGGCCTTGGAGCACTGTGACATCACTGATGCACAGCTCTCGGCCATGCTGCCTGCC
CTGAGCCAGTGCTCCCAGCTGCGCTTCCTCAGCTTCTATGGAAACCACATCTCCGTGGCCGCCCTGCACAACCTGCTGCG
CCACACTGCCAGGCTGGGCCATTTAAGCCGAGGGCTCTACCCGGCCCCTCTGGAGAGCTAC

Alignment

ORF - retro_dord_231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.36 %
• Parental protein coverage: 89.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSTMSLPTLWQLAMQSLLEDQALAISALDVLPLDLFSTLFREVVAKRRMEVLKAMVQAWPFACLPLGALV
          .S....PTL..LA.QSLL.....AIS.L..LP..LF..LF.EV.A..R.EVLKAMVQAWPF.CLPLG.L.
Retrocopy MSIRTPPTLQHLALQSLLSKESQAISVLEDLPVLLFPPLFMEVYAQGRTEVLKAMVQAWPFPCLPLGDLA

Parental  GSADLEILQVTLEGLEVLL--EQGAGPRCKLQVLDLQNRSLNIWTSGYIAMSQACSAAA-LTDKPAANHC
          .S.DLE.....L.GL..LL........R.KLQV.DL......IW..GY..M.Q..S....LT..P.....
Retrocopy ESPDLETFKAVLDGLDLLLLAKKERPRRWKLQVVDLRKAHPEIWIRGYPSMAQISSPHV>LTERPTDSRL

Parental  TDLREEPPFRIFMDVTISDGPWDYVLVHLLQWVETRRDQVQLCSKKLQVLFASTCQI-KALLMLHLDSIQ
          ....EE.P.....D.T..DG..D.....LLQW...R...VQLCS.KLQ.L..S...I.KAL....LDSIQ
Retrocopy SAGTEEQPLILAIDLTVRDGTQDAFQAYLLQWARKRKGRVQLCSTKLQILSGSIYKIQKALHAVRLDSIQ

Parental  ELVVDDLWHHKTLESMVPYLGQMKNLCKLSLATMKMECSCTS-ENL---RKYLSELLQQGNPQSMNLG--
          ELVV...WH..T.....P.L.QM.NLC.L....M.......S..NL...RKY...L.Q....Q.......
Retrocopy ELVVNNFWHRETMRKFAPSLDQMRNLCLLTFSKMSVDFYTSSRRNLWYSRKYAAHLGQLQHLQELRVHDV

Parental  LFRYENLDEVFRDPQASDQSVISS-PLNEADLRCLSLCPCTSQLKHLRLRTVNLGDLGPGPLRALLERVS
          .F.Y..L...............SS.PL.EADLR.L..CPCT.QLKHLRLR....G...P.PLRALLE.V.
Retrocopy FFLYGRLPAILSSLTPLNTLSLSSCPLKEADLRFLCQCPCTRQLKHLRLRSLCMGRFSPEPLRALLEQVA

Parental  GTLEALALEHCGITEAQLSAILPSLSQCCQLSFFSIYGNRMSLSALQNLLSHTARLRQLQRGLYPAPVES
          GTLE.LALEHC.IT.AQLSA.LP.LSQC.QL.F.S.YGN..S..AL.NLL.HTARL..L.RGLYPAP.ES
Retrocopy GTLETLALEHCDITDAQLSAMLPALSQCSQLRFLSFYGNHISVAALHNLLRHTARLGHLSRGLYPAPLES

Parental  Y
          Y
Retrocopy Y

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_231 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013324	1 retrocopy	retro_dord_231 ,
Homo sapiens	ENSG00000187545	1 retrocopy	retro_hsap_220,
Mus musculus	ENSMUSG00000025839	1 retrocopy	retro_mmus_557,
Otolemur garnettii	ENSOGAG00000000273	2 retrocopies	retro_ogar_1100, retro_ogar_1238,
Ochotona princeps	ENSOPRG00000009716	1 retrocopy	retro_opri_661,
Pan troglodytes	ENSPTRG00000029629	1 retrocopy	retro_ptro_330,
Rattus norvegicus	ENSRNOG00000042820	1 retrocopy	retro_rnor_1371,
Rattus norvegicus	ENSRNOG00000048835	1 retrocopy	retro_rnor_396,