RetrogeneDB ID: retro_hsap_3633

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:93597632..93598080(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000219387
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSG00000123268
• Aliases: ATF1, EWS-ATF1, FUS/ATF-1, TREB36
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_hsap_3633
TCTTTATCAGAAGGTGAGGAGTCTCAGGACCCATCTGACAGCTTAGGCTCTTTACAGAAAGCCTACAGGATCCTAGCACG
GCATTCATCTTACAGAAAAATTTTAAAAGACCTATCTTCTGAAGATATATGGGGCAGAAAAGGAGATGGAGAAAACCCTG
GAGTTTTTGCTGTCACTTCTGTCTGTTCCCACTCCTATCTATCAGAAGGGCAGCAAATAGTACATTGCCATTGTCTCAAG
TGGAGACTCACCATTGGCCAGTTCAGGCACAGCTGGAGTACAGAGACTTCAGACATAATTAACCATGACAAATTCAGGCA
ATACTCAGCAAGGTACAACTATTCTCCAGCATATGCAGGTCCCTGATGGACAGCAAATACTTGCATCCAGCAATCAGTTG
GTTGTACAGACTGCATCAGGTGATAGGCAGATATATCAGATCCAAACT

Alignment

ORF - retro_hsap_3633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.74 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLSESEESQDSSDSIGSSQKAHGILARRPSYRKILKDLSSEDTRGRKGDGENSGVSA-AVTSMSVPTPIY
          SLSE.EESQD.SDS.GS.QKA..ILAR..SYRKILKDLSSED..GRKGDGEN.GV.A....S...P..IY
Retrocopy SLSEGEESQDPSDSLGSLQKAYRILARHSSYRKILKDLSSEDIWGRKGDGENPGVFA>SLLSVPTP--IY

Parental  QTSSGQYIAIAPNGALQLASPGTDGVQGLQT-LTMTNSGSTQQGTTILQYAQTSDGQQILVPSNQVVVQT
          Q..S..YIAI...G...LAS.GT.GVQ.LQT.LTMTNSG.TQQGTTILQ..Q..DGQQIL..SNQ.VVQT
Retrocopy QKGSK*YIAIVSSGDSPLASSGTAGVQRLQT*LTMTNSGNTQQGTTILQHMQVPDGQQILASSNQLVVQT

Parental  ASGDMQTYQIRT
          ASGD.Q.YQI.T
Retrocopy ASGDRQIYQIQT

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	27.91 RPM
bodymap2_adrenal	0.00 RPM	27.51 RPM
bodymap2_brain	0.00 RPM	8.58 RPM
bodymap2_breast	0.00 RPM	25.06 RPM
bodymap2_colon	0.00 RPM	28.15 RPM
bodymap2_heart	0.00 RPM	18.02 RPM
bodymap2_kidney	0.00 RPM	37.18 RPM
bodymap2_liver	0.00 RPM	12.48 RPM
bodymap2_lung	0.00 RPM	30.06 RPM
bodymap2_lymph_node	0.00 RPM	41.50 RPM
bodymap2_ovary	0.00 RPM	46.65 RPM
bodymap2_prostate	0.00 RPM	39.59 RPM
bodymap2_skeletal_muscle	0.00 RPM	26.48 RPM
bodymap2_testis	0.00 RPM	31.97 RPM
bodymap2_thyroid	0.00 RPM	43.03 RPM
bodymap2_white_blood_cells	0.00 RPM	49.85 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3633 was not detected

EST

No EST(s) were mapped for retro_hsap_3633 retrocopy.

TSS

No TSS is located nearby retro_hsap_3633 retrocopy 5' end.

Lab

retro_hsap_3633 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3633 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332, retro_eeur_704,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633 ,
Mus musculus	ENSMUSG00000023027	1 retrocopy	retro_mmus_3609,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383,
Otolemur garnettii	ENSOGAG00000026029	1 retrocopy	retro_ogar_1378,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303, retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635,