RetrogeneDB ID: retro_sscr_38

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 9:6764723..6765311(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000014789
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SSU72
• Ensembl ID: ENSSSCG00000003348
• Aliases: None
• Description: SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]

Sequence

>retro_sscr_38
ATGCCATCCTCGGCCCCGCTCAGGGTGGCCGTGGTCTGCATGAGCAACATGAACAGGAGCATGGAGGCCCACAGCATCCT
CAGCAAGAAAGGCTTCCGCGTCAGGTCCTTCGGAGCGGGCTCCATGGTGAGGCTCCCGGGACCCGCCCACCACCGCCCGG
TGCTCTACAGCTTCCGCACCCCTTACCGGCAGATGCGCAGGGACCTCGCGTGGCTAGACCCAGACTGCTATCGAAGGAAC
GGCATCTTACACCTGCTGGGGAGAAACGAGCGCATCAAGCCATGCCCGGAGCGGTTTCAGGACTGCAGAGAAGCCTTCGA
TGTCATCTTCACGTGCGAGGAGAGCGTCTACGACAGGGTGGTGGGCCACCTGTGTGCCCGGGAACAGGAGACGTGCCAGC
CCGTGCACGTGATCAACGTGGACATGCAGGACGACCTGGAGGACGCCACGCTGGGGTCGCTGGTCATCTGTGAGCTGTGC
CAACGCCTGCAGCAGGCGGAGGACATGGAAGACTGCCTGGCCGAGCTGCTCCTGGGGGTGGAGCGGAAAACCGGCAGGAG
CTTTCTCCACACGGTCTGCTTCTACTGA

Alignment

ORF - retro_sscr_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSS-PLRVAVVCSSNQNRSMEAHNILSKRGFSVRSFGTGTHVKLPGPAPDKPNVYDFRTTYDQMYNDLL
          MPSS.PLRVAVVC.SN.NRSMEAH.ILSK.GF.VRSFG.G..V.LPGPA...P..Y.FRT.Y.QM..DL.
Retrocopy MPSSAPLRVAVVCMSNMNRSMEAHSILSKKGFRVRSFGAGSMVRLPGPAHHRPVLYSFRTPYRQMRRDLA

Parental  RKDKELHYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVIN
          ..D....Y..NGILH.L.RN.RIKP.PERFQ.C...FD.I.TCEE.VYD.VV..L..REQETCQPVHVIN
Retrocopy WLDPDC-YRRNGILHLLGRNERIKPCPERFQDCREAFDVIFTCEESVYDRVVGHLCAREQETCQPVHVIN

Parental  VDIQDNHEEATLGAFLICELCQCIQHTEDMENEIDELLQEFEEKSGRAFLHTVCFY
          VD.QD..E.ATLG...ICELCQ..Q..EDME....ELL...E.K.GR.FLHTVCFY
Retrocopy VDMQDDLEDATLGSLVICELCQRLQQAEDMEDCLAELLLGVERKTGRSFLHTVCFY

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
SRP014902_placenta	0.00 RPM	116.54 RPM
SRP014902_testis	0.14 RPM	56.58 RPM
SRP018288_heart	0.00 RPM	20.33 RPM
SRP018288_kidney	0.00 RPM	53.98 RPM
SRP018288_liver	0.00 RPM	40.14 RPM
SRP018288_lung	0.00 RPM	49.08 RPM
SRP018856_adipose	0.00 RPM	66.46 RPM
SRP035408_brain	0.00 RPM	87.34 RPM
SRP035408_liver	0.00 RPM	61.65 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_38 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_38 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_38 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_747
Pan troglodytes	retro_ptro_531

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013736	3 retrocopies	retro_amel_1930, retro_amel_292, retro_amel_84,
Canis familiaris	ENSCAFG00000019254	2 retrocopies	retro_cfam_185, retro_cfam_42,
Callithrix jacchus	ENSCJAG00000010957	3 retrocopies	retro_cjac_1640, retro_cjac_2335, retro_cjac_37,
Cavia porcellus	ENSCPOG00000002238	2 retrocopies	retro_cpor_83, retro_cpor_909,
Dipodomys ordii	ENSDORG00000011714	1 retrocopy	retro_dord_433,
Homo sapiens	ENSG00000160075	8 retrocopies	retro_hsap_3778, retro_hsap_4741, retro_hsap_747, retro_hsap_748, retro_hsap_749, retro_hsap_841, retro_hsap_842, retro_hsap_843,
Gorilla gorilla	ENSGGOG00000004421	1 retrocopy	retro_ggor_206,
Loxodonta africana	ENSLAFG00000002076	4 retrocopies	retro_lafr_1153, retro_lafr_1154, retro_lafr_1155, retro_lafr_400,
Macropus eugenii	ENSMEUG00000015170	1 retrocopy	retro_meug_1253,
Myotis lucifugus	ENSMLUG00000016517	2 retrocopies	retro_mluc_292, retro_mluc_371,
Macaca mulatta	ENSMMUG00000001551	1 retrocopy	retro_mmul_159,
Monodelphis domestica	ENSMODG00000006616	3 retrocopies	retro_mdom_16, retro_mdom_1997, retro_mdom_487,
Mustela putorius furo	ENSMPUG00000014394	2 retrocopies	retro_mputfur_108, retro_mputfur_1408,
Mus musculus	ENSMUSG00000029038	1 retrocopy	retro_mmus_1317,
Otolemur garnettii	ENSOGAG00000024430	2 retrocopies	retro_ogar_124, retro_ogar_13,
Pongo abelii	ENSPPYG00000002000	1 retrocopy	retro_pabe_53,
Pan troglodytes	ENSPTRG00000000034	16 retrocopies	retro_ptro_2560, retro_ptro_2963, retro_ptro_3016, retro_ptro_3017, retro_ptro_3018, retro_ptro_3019, retro_ptro_3020, retro_ptro_3021, retro_ptro_3022, retro_ptro_3023, retro_ptro_3024, retro_ptro_3025, retro_ptro_3026, retro_ptro_3156, retro_ptro_531, retro_ptro_532,
Pteropus vampyrus	ENSPVAG00000017695	4 retrocopies	retro_pvam_11, retro_pvam_1151, retro_pvam_272, retro_pvam_767,
Rattus norvegicus	ENSRNOG00000017829	2 retrocopies	retro_rnor_1169, retro_rnor_2766,
Sus scrofa	ENSSSCG00000003348	2 retrocopies	retro_sscr_1179, retro_sscr_38 ,
Ictidomys tridecemlineatus	ENSSTOG00000002960	4 retrocopies	retro_itri_1055, retro_itri_1352, retro_itri_1496, retro_itri_99,
Tursiops truncatus	ENSTTRG00000017051	2 retrocopies	retro_ttru_1264, retro_ttru_1265,