RetrogeneDB ID: retro_rnor_1428

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:38073117..38074365(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050989
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Sept7
• Ensembl ID: ENSRNOG00000006545
• Aliases: Sept7, Cdc10
• Description: septin-7 isoform a [Source:RefSeq peptide;Acc:NP_072138]

Sequence

>retro_rnor_1428
GCTCAACCGAAGAACCTTGAGGGCTATGTGGGATTTGCCATCCTCCCAAATCAAGTGTACAGAAAATCGGTGAAAAGAGG
ATTTGAATTCACTCTTATGGTAGTAGGTGAATCTGGACTGGAAAAGTCGACATTAATCAACTCATTATTCCTCACAGATT
TGTATTCTCTAGAGTATCCAGGACCTTCTCATAGAATCAAAAAGACTGTACAGGTGGAGCAATCCAAAGTTTTAGTCAAA
GAAGGTGGTGTTCAGTCGCTGCTGACGATAGTTGATACTCCGGGACTTGGAGGTGCAGTGGATAATAGTAATTGCTGGCA
GCCTGTTATCGACTACATTGATAGTAAATTTGAAGATTACTTAAATGCAGAATCTCGAGTGAACAGACGACAGATGCCTG
ATAACAGGGTGCAGTGTTGTTTATACTTCATTGCTCCTTCAGGACATGGACTTAAATCATTGGATATTGAGTTTATGAAA
CGTTTGCATGAAAAAGTGAATATCATCCCTTTAATTGCCAAAGCAGACACACTTACACCAGAGGAATGCCAACAGTTTAA
AAAGCAGATAATGAAAGAAATCCAAGAACATAAAATTAAAATATATGAATTTCCAGAAACGGATGATGAAGAAGAGAATA
AGCTGGTTAAGAAGATAAAGGACCGTTTACCTCTTGCTGTGGTGGGTAGTAATACTATCATTGAAGTTAATGGCAAAAGA
GTCAGAGGAAGGCAGTATCCTTGGGGCGTGGCTGAAGTTGAAAATGGTGAGCATTGTGATTTTACAATTCTAAGAAATAT
GTTGATACGAACACACATGCAGGACTTGAAAGATGTTACCAATAACGTACACTATGAGAACTACAGAAGCAGAAAACTAG
CAGCAGTGACCTACAATGGAGTAGATAACAACAAGAACAAAGGGCAACTTACCAAGAGCCCTCTGGTGCAGATGGAGGAG
GAGAGAAGGGAGCACGTGGCCAAGATGAAGAAGATGGAGATGGAGATGGAGCAGGTGTTTGAGATGAAGGTCAAGGAAAA
AGTTCAAAAGCTGAAGGACTCTGAAGCCGAGCTCCAGCGGCGCCATGAGCAAATGAAAAAGAATTTAGAAGCACAGCACA
AAGAATTAGAGGAAAAACGTCGTCAGTTTGAAGAAGAAAAAGCAAACTGGGAAGCTCAACAACGTATTTTAGAGCAACAG
AATTCTTCAAGAACCTTGGAAAAGAACAAGAAGAAAGGCAAGATCTTT

Alignment

ORF - retro_rnor_1428 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.91 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQPKNLEGYVGFANLPNQVYRKSVKRGFEFTLMVVGESGLGKSTLINSLFLTDLYSPEYPGPSHRIKKTV
          .QPKNLEGYVGFA.LPNQVYRKSVKRGFEFTLMVVGESGL.KSTLINSLFLTDLYS.EYPGPSHRIKKTV
Retrocopy AQPKNLEGYVGFAILPNQVYRKSVKRGFEFTLMVVGESGLEKSTLINSLFLTDLYSLEYPGPSHRIKKTV

Parental  QVEQSKVLIKEGGVQLLLTIVDTPGFGDAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCC
          QVEQSKVL.KEGGVQ.LLTIVDTPG.G.AVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCC
Retrocopy QVEQSKVLVKEGGVQSLLTIVDTPGLGGAVDNSNCWQPVIDYIDSKFEDYLNAESRVNRRQMPDNRVQCC

Parental  LYFIAPSGHGLKPLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDE
          LYFIAPSGHGLK.LDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDE
Retrocopy LYFIAPSGHGLKSLDIEFMKRLHEKVNIIPLIAKADTLTPEECQQFKKQIMKEIQEHKIKIYEFPETDDE

Parental  EENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVT
          EENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVT
Retrocopy EENKLVKKIKDRLPLAVVGSNTIIEVNGKRVRGRQYPWGVAEVENGEHCDFTILRNMLIRTHMQDLKDVT

Parental  NNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKSPLAQMEEERREHVAKMKKMEMEMEQVFEMKVKEKVQK
          NNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKSPL.QMEEERREHVAKMK.......QVFEMKVKEKVQK
Retrocopy NNVHYENYRSRKLAAVTYNGVDNNKNKGQLTKSPLVQMEEERREHVAKMKXXXXXXXQVFEMKVKEKVQK

Parental  LKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEEEKANWEAQQRILEQQNSSRTLEKNKKKGKIF
          LKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEEEKANWEAQQRILEQQNSSRTLEKNKKKGKIF
Retrocopy LKDSEAELQRRHEQMKKNLEAQHKELEEKRRQFEEEKANWEAQQRILEQQNSSRTLEKNKKKGKIF

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	0.07 RPM	146.38 RPM
SRP017611_kidney	0.00 RPM	37.40 RPM
SRP017611_liver	0.00 RPM	17.82 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1428 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012276	2 retrocopies	retro_cjac_1259, retro_cjac_3809,
Echinops telfairi	ENSETEG00000015624	3 retrocopies	retro_etel_1263, retro_etel_282, retro_etel_517,
Homo sapiens	ENSG00000122545	2 retrocopies	retro_hsap_3810, retro_hsap_4202,
Gorilla gorilla	ENSGGOG00000001175	1 retrocopy	retro_ggor_2816,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Nomascus leucogenys	ENSNLEG00000001673	1 retrocopy	retro_nleu_2152,
Otolemur garnettii	ENSOGAG00000006015	1 retrocopy	retro_ogar_1193,
Pongo abelii	ENSPPYG00000017639	1 retrocopy	retro_pabe_3438,
Pan troglodytes	ENSPTRG00000019080	2 retrocopies	retro_ptro_2585, retro_ptro_2853,
Rattus norvegicus	ENSRNOG00000006545	9 retrocopies	retro_rnor_1424, retro_rnor_1425, retro_rnor_1426, retro_rnor_1427, retro_rnor_1428 , retro_rnor_1431, retro_rnor_1445, retro_rnor_1446, retro_rnor_821,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Sarcophilus harrisii	ENSSHAG00000003788	1 retrocopy	retro_shar_258,
Ictidomys tridecemlineatus	ENSSTOG00000021378	3 retrocopies	retro_itri_1332, retro_itri_1736, retro_itri_1771,