RetrogeneDB ID: retro_dord_298

Retrocopy location

• Organism: Kangaroo rat (Dipodomys ordii)
• Coordinates: scaffold_105175:1191..2184(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gpaa1
• Ensembl ID: ENSDORG00000008463
• Aliases: None
• Description: GPI anchor attachment protein 1 [Source:MGI Symbol;Acc:MGI:1202392]

Sequence

>retro_dord_298
CAGGACTTCGCCACTCACCATAGGACGTCAGGGGCTCTGCCTGTGGCCTGGCTAGAGCGGACAATACAGTCAGTAGGGCT
GTAGGTCTACATGCAGAGTTTCTCCCAGAAACTGTCCTTTCCTGGTAAGACCCATGAGCACTATATGGTGTCGGGCACTA
ATGTGTATGGTATTCTTCGGGCCATGCATGCTGCCATCACCAAGTCCCTAGTATTCACGGCACCCTGTGGCCCAGAATCT
ACCAATAGCCAGGCTGTGGGGCTGCTGTTGGCACTTGTATCCCATTTCCAAGGTCAGATTTACTGGGTCAAAAATATCAT
CTTTCTTGTGACAGAGCATGACCTTCTGGGCACTGAGGCTGGGCTTGAAGCTTATCACAATGTCAATGTCATTGTCATGC
AGTCCTCCACTCTGCAGGGCCAAGCAGGCTCCATCCAGGTGGCTGTGGCCCTGAAGCTGAGCAGTGACATGGCTGTGGAA
GGACTCAGTGGGCAGCTGCCCAACCTTGATCTGCTCAACCTATTCCAGACCTTCTGCCAGAAAGGCAGGCTGCTGTGTTC
ACTTCAGGGCAAGCTGCAACCTCAGGACGAGACACTGATGGATGGGTCACTGCAAAGCCTGCAGACGCTGCTGCTTATGT
TTCCTCGGGAGGCCTCTGGCCACCGTCACTGCCCCCATGGCCTCTTCCTACACTTCTGGGTAGAGGCTCTGAGCCTGCAT
GGTATCAGTTGCTTCCGCCAGTACATGTGTGACTTGGTGGCAGTGGGAAAGGGTCTAGAGGGTATGTTCCTCAAGCTCAA
CCACCTCCTGGAGTGCCTGTAACAGTCATTCTTCTTCGACCTGAGGCCTGGTCTCTCCTGCTTCGTTTCCATTGGCCTCT
ACATACTCATGGCTGGCTTCTTGCTCCTGGTCCTAGGACTCATGGCTCTAGAGCTACAGATGCAGCTGAACAAGCCTGGC
AACCACCCCTACCCCCAGCACAGGGTGTGGGGC

Alignment

ORF - retro_dord_298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.62 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RDFAAHRRKSGALPVAWLERTMRSVGLEVYTQSFSRKLPFPDETHERYMVSGTNVYGILRAPRAASTESL
          .DFA.H.R.SGALPVAWLERT..SVGL.VY.QSFS.KL.FP..THE.YMVSGTNVYGILRA..AA.T.SL
Retrocopy QDFATHHRTSGALPVAWLERTIQSVGL*VYMQSFSQKLSFPGKTHEHYMVSGTNVYGILRAMHAAITKSL

Parental  VLTVPCGPESTNSQAVGLLLALASHFRGQIYWAKDIIFLVTEHDLLGTEAWLEAYHDVNVTGMQSSPLQG
          V.T.PCGPESTNSQAVGLLLAL.SHF.GQIYW.K.IIFLVTEHDLLGTEA.LEAYH.VNV..MQSS.LQG
Retrocopy VFTAPCGPESTNSQAVGLLLALVSHFQGQIYWVKNIIFLVTEHDLLGTEAGLEAYHNVNVIVMQSSTLQG

Parental  RAGSIQAAVALELSSDVVTSLDVAVEGLNGQLPNLDLLNLFQTFCQKGGLLCTLQGKLQPQDWTSVDGPL
          .AGSIQ.AVAL.LSSD..........G....L..L.L...F...CQKG.LLC.LQGKLQPQD.T..DG.L
Retrocopy QAGSIQVAVALKLSSDMAVE---GLSGQLPNLDLLNLFQTF---CQKGRLLCSLQGKLQPQDETLMDGSL

Parental  QSLQTLLLMVLRQASGRPHGPHGLFLRYRVEALTLRGINSFRQYKYDLVAVGKALEGMFRKLNHLLERLH
          QSLQTLLLM..R.ASG..H.PHGLFL...VEAL.L.GI..FRQY..DLVAVGK.LEGMF.KLNHLLE.L.
Retrocopy QSLQTLLLMFPREASGHRHCPHGLFLHFWVEALSLHGISCFRQYMCDLVAVGKGLEGMFLKLNHLLECL*

Parental  QSFFFYLLPALSRFVSIGLYMPAAGFLLLVLGLKALELWMQLHEAGVDPGEAGRASG
          QSFFF.L.P.LS.FVSIGLY...AGFLLLVLGL.ALEL.MQL...G..P....R..G
Retrocopy QSFFFDLRPGLSCFVSIGLYILMAGFLLLVLGLMALELQMQLNKPGNHPYPQHRVWG

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_298 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021455	1 retrocopy	retro_cjac_1889,
Dipodomys ordii	ENSDORG00000008463	1 retrocopy	retro_dord_298 ,