RetrogeneDB ID: retro_rnor_862

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:13797211..13798063(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000048886
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dppa4
• Ensembl ID: ENSRNOG00000025404
• Aliases: None
• Description: Developmental pluripotency-associated protein 4 [Source:UniProtKB/Swiss-Prot;Acc:D3Z8Y2]

Sequence

>retro_rnor_862
GCAGAGGAGCCAAGGGAAGAAGTGGAATGCCAGATGTCTAGCCAACCGAGCACGTCTTCTGCAAAGACTAAAGCAACGGG
GAAGAAACAAAGAAAGTCAGAGAAAGATGACGGTTGTAAACCAGAGGAGAAAAGTGCACAAGATCCTGAGACTCCAGGGC
ACACTCGTAGGAAGGTACCTGTTCCTCCTTTTCCACAGCATCTGCCCCCCGTGAACCTGATTCACCGAGACGTTTTGCGG
GCCTGGTGCCAGGAGATGAAGCTGAGCAGCAAAGGCCAGAAATTAGATGCTTATAAACGACTCCTTGCAAGGGCTTTCCC
AGATCAAATGCCCGAGTTGAAGAATGTTCCTGACTCAGCCAAAGAGGCCAGGTTGAAGATGCCTCGGAAAAAAATGAAGA
CGGAACCTGGGGAAGAGTCTCAGGTGACAGTTCCCCTGGAGATCGTCACTGTACCAGAGGAGCAGATACCTGCTCTCGTT
GATCCTCCTGTGCTCTATGAGGAAGTCAGCACCACGGTGGTAACTACATCTGCCTCAGAGGCAGTGTTGGCATCTTGGGC
CAGAATAGCAGCCAATGCTAAGAAGTTGGAGGCAGTGCCTTCCAATGCAACATCGGAGACCTATGGGGAAATGTGGTGTG
TGGTGCATGGGACAAGCCTTCCCGCAACCTCAAGTGGTTGGGTTCGACTACAGTTCCATGCTGGATAAGCCTGGGTACCC
GATAAGAAAGGGAAAGCGATTGCCCTCTTCCTGCTTCCGGCCTGCACATTTCCGCCCCCACACCTGGAGGATAACATGCT
GTGCCCCAAGTGTGTTCATAGGAACAAGGTCTTAACTAAGAGCCTTGAAGGA

Alignment

ORF - retro_rnor_862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEEPREEVECQMSSQPSTSSAKTKATGKKQRKSEKDDGCKPEEKSAQDPETPGHARRKVPVPPFPQHLPP
          AEEPREEVECQMSSQPSTSSAKTKATGKKQRKSEKDDGCKPEEKSAQDPETPGH.RRKVPVPPFPQHLPP
Retrocopy AEEPREEVECQMSSQPSTSSAKTKATGKKQRKSEKDDGCKPEEKSAQDPETPGHTRRKVPVPPFPQHLPP

Parental  VNLIHRDVLRAWCQEMKLSSKGQKLDAYKRLLARAFPDQMPELKNVPDSAKEARLKMPRKKMKTEPGEES
          VNLIHRDVLRAWCQEMKLSSKGQKLDAYKRLLARAFPDQMPELKNVPDSAKEARLKMPRKKMKTEPGEES
Retrocopy VNLIHRDVLRAWCQEMKLSSKGQKLDAYKRLLARAFPDQMPELKNVPDSAKEARLKMPRKKMKTEPGEES

Parental  QVTVPLEIVTVPEEQIPALVDPPVLYEEVSTTVVTTSASEAVLASWARIAANAKKLEAVPSNATSETYGE
          QVTVPLEIVTVPEEQIPALVDPPVLYEEVSTTVVTTSASEAVLASWARIAANAKKLEAVPSNATSETYGE
Retrocopy QVTVPLEIVTVPEEQIPALVDPPVLYEEVSTTVVTTSASEAVLASWARIAANAKKLEAVPSNATSETYGE

Parental  MWCVVHGTSLPATSSGWVRLQFHAGQAWVPDKKGKAIALFLLPACTFPPPHLEDNMLCPKCVHKNKILTK
          MWCVVHGTSLPATSSGWVRLQFHAG.AWVPDKKGKAIALFLLPACTFPPPHLEDNMLCPKCVH.NK.LTK
Retrocopy MWCVVHGTSLPATSSGWVRLQFHAG*AWVPDKKGKAIALFLLPACTFPPPHLEDNMLCPKCVHRNKVLTK

Parental  SLEG
          SLEG
Retrocopy SLEG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.21 RPM
SRP017611_liver	0.00 RPM	0.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_862 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_862 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010335	5 retrocopies	retro_cfam_1332, retro_cfam_1540, retro_cfam_1905, retro_cfam_1934, retro_cfam_996,
Callithrix jacchus	ENSCJAG00000020171	2 retrocopies	retro_cjac_1334, retro_cjac_1491,
Echinops telfairi	ENSETEG00000002722	1 retrocopy	retro_etel_312,
Homo sapiens	ENSG00000121570	1 retrocopy	retro_hsap_893,
Gorilla gorilla	ENSGGOG00000015121	2 retrocopies	retro_ggor_1970, retro_ggor_723,
Loxodonta africana	ENSLAFG00000016804	1 retrocopy	retro_lafr_456,
Myotis lucifugus	ENSMLUG00000016423	1 retrocopy	retro_mluc_973,
Macaca mulatta	ENSMMUG00000016901	1 retrocopy	retro_mmul_1515,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mustela putorius furo	ENSMPUG00000010206	1 retrocopy	retro_mputfur_800,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Nomascus leucogenys	ENSNLEG00000004030	3 retrocopies	retro_nleu_2888, retro_nleu_3018, retro_nleu_388,
Oryctolagus cuniculus	ENSOCUG00000016435	1 retrocopy	retro_ocun_114,
Pongo abelii	ENSPPYG00000013565	3 retrocopies	retro_pabe_2316, retro_pabe_2349, retro_pabe_770,
Pan troglodytes	ENSPTRG00000015200	2 retrocopies	retro_ptro_1923, retro_ptro_616,
Pteropus vampyrus	ENSPVAG00000010677	1 retrocopy	retro_pvam_1237,
Rattus norvegicus	ENSRNOG00000025404	4 retrocopies	retro_rnor_2750, retro_rnor_2996, retro_rnor_861, retro_rnor_862 ,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tursiops truncatus	ENSTTRG00000009508	1 retrocopy	retro_ttru_1772,