RetrogeneDB ID: retro_rnor_1752

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:5200754..5201476(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Srsf6
• Ensembl ID: ENSRNOG00000006380
• Aliases: Srsf6, Sfrs6
• Description: splicing factor, arginine/serine-rich 6 [Source:RefSeq peptide;Acc:NP_001014207]

Sequence

>retro_rnor_1752
TTTCAGCGCCTCCTGGAAATCGACCTAGAAAACGGGTAAGGTTTCGTGGAGTTTCGAGGACTCCCGTGATGCGGACGAGC
TGAACAGCAAGGAGCTGTGCGGCCGGTTCGTGATGGTCGCGCGCTCCCGGGGCGGCGCCGCGACCGTGATGGCTACAGCT
ACAGACGCCGCTGTGGTAGAGTTGGACACAGCAGTCGGAGAACTTCTGGCAGAGGCACATATGGAACAGCTATTCGTACA
GAATACAGACTTATTGTCGAAAATCTGTCTAGTCGCCGCAGTTGGCAAGACTTGAAGGATTTCATGCGGCAAGCAGGAGA
GGTGACTTCTGCAGATGCTCACAAAGAACGAACAAATGAGGGTGCAATTGAATTTAGATCCTACTCTGACAGGAAGCGTG
CGTTGGATAAACCGGATGGCACAGAAATAAATGGCAGAAATTCTACCTTCAATAAGCCACGAACAAAGTCATAGGCGCTC
TGACTCTGGAAGTAGATCACGGTCTAGAAGAAGATCTCTTGAGTAGGCGTCGCGGAAGCAGCCGCTGTAGATCTTGAAGT
ACCTCAAAAAGTCGCTCCTATCTAGGTCTCCTAGCAAATGTCAAATCTAAGCTTAGGTCTGATCCGGGTTCCCATTCGCA
CTCAGGAGGCAGATCTAAGGATAAGTGTGGGAAGCCACGAAGTAGGTCACCTTCTTGATCCCCCAAAGAAAATAGAAAAG
GA

Alignment

ORF - retro_rnor_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.87 %
• Parental protein coverage: 72.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YGRLLEIDLKNGYGFVEF-EDSRDADDAVYELNSKELCGERVIVEHARGP-RRDRDGYSYGSRSGGGGYS
          ..RLLEIDL.NG.GFVEF.EDSRDAD....ELNSKELCG..V.V...RG..RRDRDGYSY..R.G..G.S
Retrocopy FQRLLEIDLENG*GFVEF>EDSRDAD----ELNSKELCGRFVMVARSRGG<RRDRDGYSYRRRCGRVGHS

Parental  SRRTSGRDKYGPPVRTEYRLIVENLSSRCSWQDLKDFMRQAGEVTYADAHKERTNEGVIEFRSYSDMKRA
          SRRTSGR..YG...RTEYRLIVENLSSR.SWQDLKDFMRQAGEVT.ADAHKERTNEG.IEFRSYSD.KRA
Retrocopy SRRTSGRGTYGTAIRTEYRLIVENLSSRRSWQDLKDFMRQAGEVTSADAHKERTNEGAIEFRSYSDRKRA

Parental  LDKLDGTEINGRNIRLIEDKPRT-SHRRSYSGSRSRSRSRR-RSRSRSRRSSRSRSRSISKSRSRSRSRS
          LDK.DGTEINGRN......KPRT.SHRRS.SGSRSRSR.R...SR.R...SSR.RS.S.SKSRS......
Retrocopy LDKPDGTEINGRNSTF--NKPRT>SHRRSDSGSRSRSRRRS>LSRRRG--SSRCRS*STSKSRSYLGLLA

Parental  KGRSRSRS-KGRKSRSKSKSKPKSDR-GSHSHSRSRSKDKYG
          ...S..RS..G..S.S...SK.K.....S.S.S.S......G
Retrocopy NVKSKLRSDPGSHSHSGGRSKDKCGKPRSRSPS*SPKENRKG

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	84.62 RPM
SRP017611_kidney	0.00 RPM	112.56 RPM
SRP017611_liver	0.00 RPM	59.51 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1752 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1752 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002061	1 retrocopy	retro_acar_191,
Canis familiaris	ENSCAFG00000009289	1 retrocopy	retro_cfam_392,
Echinops telfairi	ENSETEG00000006221	1 retrocopy	retro_etel_1261,
Homo sapiens	ENSG00000124193	1 retrocopy	retro_hsap_1809,
Gorilla gorilla	ENSGGOG00000009808	1 retrocopy	retro_ggor_2176,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Nomascus leucogenys	ENSNLEG00000006524	1 retrocopy	retro_nleu_1294,
Oryctolagus cuniculus	ENSOCUG00000009785	1 retrocopy	retro_ocun_312,
Pongo abelii	ENSPPYG00000011019	1 retrocopy	retro_pabe_1483,
Pan troglodytes	ENSPTRG00000013506	1 retrocopy	retro_ptro_3057,
Rattus norvegicus	ENSRNOG00000000520	11 retrocopies	retro_rnor_1010, retro_rnor_1283, retro_rnor_1321, retro_rnor_1339, retro_rnor_1647, retro_rnor_1697, retro_rnor_1889, retro_rnor_2424, retro_rnor_634, retro_rnor_728, retro_rnor_790,
Rattus norvegicus	ENSRNOG00000005513	1 retrocopy	retro_rnor_2900,
Rattus norvegicus	ENSRNOG00000006380	1 retrocopy	retro_rnor_1752 ,
Rattus norvegicus	ENSRNOG00000027360	11 retrocopies	retro_rnor_1535, retro_rnor_1977, retro_rnor_1984, retro_rnor_2419, retro_rnor_2420, retro_rnor_2421, retro_rnor_2495, retro_rnor_2501, retro_rnor_2502, retro_rnor_2503, retro_rnor_478,
Tupaia belangeri	ENSTBEG00000013448	1 retrocopy	retro_tbel_383,
Tursiops truncatus	ENSTTRG00000015410	2 retrocopies	retro_ttru_1786, retro_ttru_1787,