RetrogeneDB ID: retro_hsap_4214

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:125524152..125524509(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000232387
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SKA2
• Ensembl ID: ENSG00000182628
• Aliases: SKA2, FAM33A
• Description: spindle and kinetochore associated complex subunit 2 [Source:HGNC Symbol;Acc:28006]

Sequence

>retro_hsap_4214
GCGGAGGTCGATAAGCTGGAACTGATGTTCCAGAAAGCTGAGTCTGATCTGGATTACATTCAATACAGGCTGGAATATGA
AATCAAGACTAATCATCCTGATTCAGCAAGTGAGAAAAATCCAGTTACACTCTTAAAGGAATTGTCAGTGATAAAGTCTC
AATATCAAACTTTGTATGCCCGCTTTAAACCAGTTGCTGTTGAGCAGAAAGAGACTAAGAGCCGCATTTGTGCTGGTATG
ACTAAAACTATGAATGTGATACAAAAACTACAGAAGCAAACAGACCTGGATCTGTCACCACTGACTAAAGAAGAGAAAAC
TGCGGCAGAGCAATTCAAATCTCACGTGCCAGATTTA

Alignment

ORF - retro_hsap_4214 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.44 %
• Parental protein coverage: 98.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEVDKLELMFQKAESDLDYIQYRLEYEIKTNHPDSASEKNPVTLLKELSVIKSRYQTLYARFKPVAVEQK
          AEVDKLELMFQKAESDLDYIQYRLEYEIKTNHPDSASEKNPVTLLKELSVIKS.YQTLYARFKPVAVEQK
Retrocopy AEVDKLELMFQKAESDLDYIQYRLEYEIKTNHPDSASEKNPVTLLKELSVIKSQYQTLYARFKPVAVEQK

Parental  ESKSRICATVKKTMNMIQKLQKQTDLELSPLTKEEKTAAEQFKFHMPDL
          E.KSRICA...KTMN.IQKLQKQTDL.LSPLTKEEKTAAEQFK.H.PDL
Retrocopy ETKSRICAGMTKTMNVIQKLQKQTDLDLSPLTKEEKTAAEQFKSHVPDL

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
bodymap2_adipose	0.00 RPM	16.42 RPM
bodymap2_adrenal	0.20 RPM	36.23 RPM
bodymap2_brain	0.05 RPM	53.44 RPM
bodymap2_breast	0.00 RPM	36.63 RPM
bodymap2_colon	0.00 RPM	32.33 RPM
bodymap2_heart	0.02 RPM	29.22 RPM
bodymap2_kidney	0.08 RPM	31.77 RPM
bodymap2_liver	0.00 RPM	13.07 RPM
bodymap2_lung	0.00 RPM	19.51 RPM
bodymap2_lymph_node	0.09 RPM	24.80 RPM
bodymap2_ovary	0.06 RPM	46.09 RPM
bodymap2_prostate	0.02 RPM	30.73 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.40 RPM
bodymap2_testis	0.00 RPM	35.35 RPM
bodymap2_thyroid	0.08 RPM	45.67 RPM
bodymap2_white_blood_cells	0.00 RPM	24.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4214 was not detected

EST

No EST(s) were mapped for retro_hsap_4214 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_189335	457 libraries	617 libraries	666 libraries	73 libraries	16 libraries

The graphical summary, for retro_hsap_4214 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_4214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4214 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021680	2 retrocopies	retro_btau_310, retro_btau_945,
Canis familiaris	ENSCAFG00000029233	1 retrocopy	retro_cfam_766,
Cavia porcellus	ENSCPOG00000006051	1 retrocopy	retro_cpor_542,
Dipodomys ordii	ENSDORG00000010768	2 retrocopies	retro_dord_103, retro_dord_281,
Equus caballus	ENSECAG00000015007	1 retrocopy	retro_ecab_987,
Felis catus	ENSFCAG00000022802	1 retrocopy	retro_fcat_1111,
Homo sapiens	ENSG00000182628	1 retrocopy	retro_hsap_4214 ,
Loxodonta africana	ENSLAFG00000003405	1 retrocopy	retro_lafr_1215,
Myotis lucifugus	ENSMLUG00000010942	1 retrocopy	retro_mluc_83,
Monodelphis domestica	ENSMODG00000014619	1 retrocopy	retro_mdom_347,
Mustela putorius furo	ENSMPUG00000015241	1 retrocopy	retro_mputfur_1435,
Mus musculus	ENSMUSG00000020492	2 retrocopies	retro_mmus_370, retro_mmus_778,
Otolemur garnettii	ENSOGAG00000026072	4 retrocopies	retro_ogar_1882, retro_ogar_2937, retro_ogar_3032, retro_ogar_907,
Rattus norvegicus	ENSRNOG00000025981	3 retrocopies	retro_rnor_1606, retro_rnor_523, retro_rnor_733,
Sorex araneus	ENSSARG00000011128	2 retrocopies	retro_sara_60, retro_sara_662,
Ictidomys tridecemlineatus	ENSSTOG00000024169	4 retrocopies	retro_itri_1115, retro_itri_1275, retro_itri_1434, retro_itri_725,
Tarsius syrichta	ENSTSYG00000006158	3 retrocopies	retro_tsyr_1620, retro_tsyr_2034, retro_tsyr_748,
Tursiops truncatus	ENSTTRG00000017196	1 retrocopy	retro_ttru_143,