RetrogeneDB ID: retro_rnor_1306

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:47626448..47626932(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zwint
• Ensembl ID: ENSRNOG00000048682
• Aliases: Zwint, Sip30, Zwint-1
• Description: ZW10 interactor [Source:UniProtKB/Swiss-Prot;Acc:Q8VIL3]

Sequence

>retro_rnor_1306
TCAAAGGTCATGGGAGAGTTTGTGAGGGACTCTCGGGAGAAAGGTAGTTGCTTTGCTTGTTCTTGAAAGTAGTAAACTTC
TTACAGCATCTTCTGGCTCAGAAGAATAACACAGCCCAGAACCCAGACACTTTGGTTTCTGAAAATATAAGTTGACCAAG
GCAACCGAAGCTAAGGAACACTGGAAGTAACTTGAGGCCACATATCTGGATCATGTGGACACCAGGAGATGTGCCCTGAC
CCAGGTCTTACCCCAGGTAAGAGGCTCAAAGGAAGTACACAGAGCTTCAGAAGGCTTTTGAGAACTCCAGGCCGAGAAGC
AAGTACTTGAGGAGAAACTTCAATAGGCTCAGAAGCGGTGGCAGCTGCAACAGAAGCCTTTGCAGAGTCTGACAAAGATT
TCTGCAAAGGTAAAGGGAGGTCAAAAGAGAGTTCTGGAGAAGCTTGACAGATCACACTGGGAACTTGAAATCTTGAAGCA
GGAG

Alignment

ORF - retro_rnor_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.39 %
• Parental protein coverage: 61.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKIMEEFMRNSRKKDK-LLCSQLQVVNFLQTFLAQEDNTDQNPDALASEDTS-RQKATETKEQWKELKAT
          .K.M.EF.R.SR.K...LLC..L.VVNFLQ..LAQ..NT.QNPD.L.SE..S...KATE.KE.WK.L.AT
Retrocopy SKVMGEFVRDSREKGS<LLCLFLKVVNFLQHLLAQKNNTAQNPDTLVSENIS<LTKATEAKEHWK*LEAT

Parental  YMDHVDVIKCALSEALPQVKEAHRKYTELQKAFEQLEAKKRVLEEKLQLAQKQWVLQQKRLQNLTKISAE
          Y.DHVD...CAL...LPQV.............F..L.A.K.VLEEKLQ.AQK.W.LQQK.LQ.LTKISA.
Retrocopy YLDHVDTRRCALTQVLPQVR-GSKEVHRASEGF*ELQAEKQVLEEKLQ*AQKRWQLQQKPLQSLTKISAK

Parental  VKRRRKRALEKLDGSHQELETLKQQ
          VK...KR.LEKLD.SH.ELE.LKQ.
Retrocopy VKGGQKRVLEKLDRSHWELEILKQE

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	2065.87 RPM
SRP017611_kidney	0.00 RPM	110.12 RPM
SRP017611_liver	0.00 RPM	22.12 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1306 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1306 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_997

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002655	1 retrocopy	retro_btau_239,
Echinops telfairi	ENSETEG00000007793	1 retrocopy	retro_etel_261,
Mus musculus	ENSMUSG00000019923	3 retrocopies	retro_mmus_1488, retro_mmus_2611, retro_mmus_997,
Rattus norvegicus	ENSRNOG00000048682	2 retrocopies	retro_rnor_1211, retro_rnor_1306 ,
Tarsius syrichta	ENSTSYG00000010283	1 retrocopy	retro_tsyr_1005,
Tursiops truncatus	ENSTTRG00000002204	1 retrocopy	retro_ttru_1193,