RetrogeneDB ID: retro_rnor_134

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:59141776..59142919(-)
• Located in intron of: ENSRNOG00000004483

Retrocopy information

• Ensembl ID: ENSRNOG00000022632
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Taf7l
• Ensembl ID: ENSRNOG00000026315
• Aliases: Taf7l, RGD1564898
• Description: transcription initiation factor TFIID subunit 7-like [Source:RefSeq peptide;Acc:NP_001129349]

Sequence

>retro_rnor_134
ATGAGTAAAAGCCAAGATGAACTTCCTCACGAACTTGAGAACCAGTTCATATTGCGCCTTCCCCCAGAACATGCTTCAAC
TGTCAGGAAGATCATACGTTCTGGAAATGCTGCCATGAGAGATAAACTAAAAATTGACTTGTCTCCTGATTCACGGCATG
CTATTGTTCAGGTAGATGACGTTTCACTGTCTGCCAAAGTTGTTGATTTGCCTTGTGTTATTGGAAGCCTGAAAACGCAC
GATAGGAAGACCTTTTATAAAACGGCCGATGTTTCCCAGATGCTTTTGTGCAGTGCCGAGGGCGATCTCCACTCTTCGCC
AGAAGAACCAGCCACTTCTGCTGGTGCTACTGTAATGGAAAACGAAAGGGAAGCAGAGGAAAAGTATATCTGGAAGCACG
GCATTACTCCACCACTTAAGAATGTCAGAAAGAAACGGTTTCGGAAACCAACAAAAAAGCCCCCTGATATGAAGCAAAAC
GGAGAAAGCTCTAGTGGTTACATTGATTCTAAAGACGTGGAGAAGGAAGTGAAGAGGCTGCTGCGCTCAGATGCCGAAGC
CATCAGCTGCCGATGGGAAATCATTGTTGATGATGAAACCAAGGCAGTACAAAGTCAAACTTGTACTCCTCATCTTCCAT
TACCCTCTGAAGTAGGTGGCCATACCTCATCAGCATGTGATATGCCTCAGAGCACATTCAGTGATTCTAGCAGTTGCAAA
GATGATCAAGAGAATAAAGAGGAGGAGGAGGAGGAGGAAAAAGAGGAGGATGAAGAGGAAGGGGAGGCTGAAGAGGAGGA
GGAAGAAGAGGAGGAAGAGGAGGAGGAGGAGGAAGATGATTCTGAAGAAGACCTGGAAAGAGAGCTACAAGCCAAGTTTA
TTGAGTTTAGCTTGTGCGAAGCTAAAGAAAGTAGCAGTTCAATAATTCTGGGAATTCAGAAGCTGATTCATTCCAAGGAG
AGAAAACTCCAAGAGATTCAGGGCAAAGCACAAAGACAGAAGGATCTCCTCAGAAAATTGGAAAACCTAACCCTCAAGAG
TCATTTTCAGTCTGTGCTGGAGCAGCTCAAGTTACAGGAGAAGCAGAAGGCTGAGCAGATCCTTTTTCTACAGCAACAAC
TGAAGTATTTTTTGAAGAAGTAA

Alignment

ORF - retro_rnor_134 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.65 %
• Parental protein coverage: 72.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRLPPVTDGHHAVVQVENVSLPAKLVNLPCVIGSLKTVDRKTFYQTADISQMLVCSPEGEPHSSPEEPVI
          L......D..HA.VQV..VSL.AK.V.LPCVIGSLKT.DRKTFY.TAD.SQML.CS.EG..HSSPEEP..
Retrocopy LKIDLSPDSRHAIVQVDDVSLSAKVVDLPCVIGSLKTHDRKTFYKTADVSQMLLCSAEGDLHSSPEEPAT

Parental  STGPTVTGHIEGKAEKKKYNWKHGITPPLKNVRKKRFRKTTKKLPDVKQMDEINFSEYTQSPSVEKEVKR
          S.G.TV....E..AE.K.Y.WKHGITPPLKNVRKKRFRK.TKK.PD.KQ..E...S.Y..S..VEKEVKR
Retrocopy SAGATVMEN-EREAEEK-YIWKHGITPPLKNVRKKRFRKPTKKPPDMKQNGESS-SGYIDSKDVEKEVKR

Parental  LLCSDAEAVSVRWEVVADDDTKEIESQGCISTTSGTPQMGGAGSSEYDVLREMMGETGSNSNDVEDKNSK
          LL.SDAEA.S.RWE...DD.TK...SQ.C..........GG..SS..D..........S...D.E.K...
Retrocopy LLRSDAEAISCRWEIIVDDETKAVQSQTCTPHLPLPSEVGGHTSSACDMPQSTFSDSSSCKDDQENKEEE

Parental  IEDEDEDDQE----DEDEDDGNEEKEEETDNSEEELEKELQAKFIQSSLHEKEQDYTSIIMEIQKLIHIK
          .E.E.E.D.E.....E.E....EE.EEE.D.SEE.LE.ELQAKFI..SL.E......SII..IQKLIH.K
Retrocopy EEEEKEEDEEEGEAEEEEEEEEEEEEEEEDDSEEDLERELQAKFIEFSLCEAKESSSSIILGIQKLIHSK

Parental  EQKLQQIYKKAQRQKDLLRNVENLTLKRHFQNVLEKLNILEKEKCEQIYHLQEQLKCFLKE
          E.KLQ.I..KAQRQKDLLR..ENLTLK.HFQ.VLE.L...EK.K.EQI..LQ.QLK.FLK.
Retrocopy ERKLQEIQGKAQRQKDLLRKLENLTLKSHFQSVLEQLKLQEKQKAEQILFLQQQLKYFLKK

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	0.29 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_134 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_134 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_72

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009247	1 retrocopy	retro_amel_6,
Bos taurus	ENSBTAG00000001979	1 retrocopy	retro_btau_107,
Loxodonta africana	ENSLAFG00000006941	1 retrocopy	retro_lafr_209,
Mus musculus	ENSMUSG00000009596	1 retrocopy	retro_mmus_72,
Oryctolagus cuniculus	ENSOCUG00000004497	1 retrocopy	retro_ocun_191,
Rattus norvegicus	ENSRNOG00000026315	1 retrocopy	retro_rnor_134 ,