RetrogeneDB ID: retro_rnor_2900

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:20825589..20826270(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Srsf5
• Ensembl ID: ENSRNOG00000005513
• Aliases: None
• Description: Serine/arginine-rich splicing factor 5 [Source:UniProtKB/Swiss-Prot;Acc:Q09167]

Sequence

>retro_rnor_2900
ATGAGTGGCTGTTGAGTGTTCATTGGGAGACTAAATCCAGCAGCGAGGGAGAAAGATGTGGAAAGATTCTTCAAGGGTTA
CGGACGGATCAGAGATATTGATTTGAAAAGAGGTTTTGGTTTTGTGGAATTCGAGGATGTAGATGACACTGTCTATGAAC
TTGATGGAAAGGCACTTTGCAGTGAAAGGGTTACTATTGAACATGCTTGGGCTCGGGCTCAAGGTGAAAGAGGTAGAGGA
CGATACTCCGACCATTTTAGCAGTCGCAGACCTCGAAATGATAGACGAAATGCCCCACCTGTAAGAACAGAAAATCGACT
TATAGTTGAGAATTTATCCTCAAGAGTCAGCTGGCAGGATCTCAAAAATTCCACGAGACAAGCTGGGGAAGTAACCTTTG
CGGATGCACATCAACCTAAACTAAATGAAGGGGTAGTTGAGTTTGCCTCTTATGGTGACTTAAAGACTGCTAGTGAGAAA
CTTTCTGGAAAGGAAATGAACGGGCGAAAAATCAAATTAATTGAAGTCAGCAAAAGGCATAGGTCAAGAAGCAGGTCACG
ATCTCTGACCAGGAGTTCCTCTAGGTCCCATAGCCAATTCCGTTTACGCAGGAGCAAGTCTCACAGTCGATCAAGGAGCA
GGAGCCGGAGCCGGAGCAAGTCCCGTTCTGGTAGTAGGTCG

Alignment

ORF - retro_rnor_2900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 85.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGCRVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDGKELCSERVTIE
          MSGC.VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFE...D.DD.VYELDGK.LCSERVTIE
Retrocopy MSGC*VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGFVEFE---DVDDTVYELDGKALCSERVTIE

Parental  HARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFADAH
          HA.AR..G.RGRGRYSD.FSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLK...RQAGEVTFADAH
Retrocopy HAWARAQGERGRGRYSDHFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKNSTRQAGEVTFADAH

Parental  RPKLNEGVVEFASYGDLKNAIEKLSGKEINGRKIKLIEGSKRHRSRSRSRSRTRSSSRSRSRSRSRRSKS
          .PKLNEGVVEFASYGDLK.A.EKLSGKE.NGRKIKLIE.SKRHRSRSRSRS.TRSSSRS.S..R.RRSKS
Retrocopy QPKLNEGVVEFASYGDLKTASEKLSGKEMNGRKIKLIEVSKRHRSRSRSRSLTRSSSRSHSQFRLRRSKS

Parental  YSRSRSRSRSRSKSRSGSRS
          .SRSRSRSRSRSKSRSGSRS
Retrocopy HSRSRSRSRSRSKSRSGSRS

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	0.14 RPM	172.34 RPM
SRP017611_kidney	0.00 RPM	192.39 RPM
SRP017611_liver	0.00 RPM	141.40 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2900 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2900 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001521	2 retrocopies	retro_meug_1173, retro_meug_2182,
Monodelphis domestica	ENSMODG00000011362	1 retrocopy	retro_mdom_934,
Mus musculus	ENSMUSG00000021134	1 retrocopy	retro_mmus_2396,
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	ENSTBEG00000001972	1 retrocopy	retro_tbel_2707,